@ncukondo/search-hub 0.7.0 → 0.9.0

package/README.md

@@ -11,6 +11,7 @@ A CLI tool for systematic literature searching across multiple academic database
 - **Unified query syntax**: YAML-based DSL with automatic translation
 - **Reproducible searches**: Full session logging for PRISMA reporting
 - **Resume support**: Continue interrupted searches at DB or page level
+- **Fulltext management**: OA discovery, automatic retrieval, PMC XML to Markdown conversion
 - **Reference manager integration**: Works with [reference-manager](https://github.com/ncukondo/reference-manager)
 
 ## Installation
@@ -114,12 +115,35 @@ Developing an effective search query is iterative. Start broad, then refine base
 
 - **Keep query versions**: Save each iteration (v1, v2, v3) to track your development process and maintain reproducibility.
 
+## Fulltext Retrieval
+
+After screening, retrieve fulltext articles for included papers:
+
+```bash
+# Check Open Access availability
+search-hub fulltext check --session <session-id>
+
+# Download available OA fulltexts (auto-converts PMC XML to Markdown)
+search-hub fulltext fetch <session-id>
+
+# For non-OA articles: create directories for manual download
+search-hub fulltext init <session-id>
+search-hub fulltext pending <session-id>
+
+# After manually adding PDFs, sync and register
+search-hub fulltext sync <session-id>
+search-hub register <session-id>
+```
+
+See [Fulltext Management Guide](./docs/fulltext.md) for details.
+
 ## Documentation
 
 - [Query Guide](./docs/query-guide.md) - How to write query files
 - [Command Reference](./docs/commands.md) - All CLI commands and options
 - [Configuration](./docs/configuration.md) - Setup and configuration
 - [Databases](./docs/databases.md) - Supported databases and tips
+- [Fulltext Management](./docs/fulltext.md) - Fulltext retrieval and management
 
 ## Development
 

package/dist/cli/commands/config.d.ts.map

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package/dist/cli/commands/config.js

@@ -43,6 +43,7 @@ function formatValue(value) {
   if (value === null) return "null";
   if (value === void 0) return "undefined";
   if (typeof value === "string") return value;
+  if (Array.isArray(value)) return JSON.stringify(value);
   if (typeof value === "object") return JSON.stringify(value, null, 2);
   return String(value);
 }

package/dist/cli/commands/config.js.map

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package/dist/cli/commands/fulltext/attach.d.ts

@@ -0,0 +1,12 @@
+import { FulltextAttachResult } from '../../../integration/types.js';
+export interface FulltextAttachCommandOptions {
+    sessionDir: string;
+    dryRun: boolean;
+    onProgress?: (current: number, total: number) => void;
+}
+/**
+ * Execute the standalone fulltext attach command.
+ * Reads the session's fulltext directories and attaches files to ref entries.
+ */
+export declare function executeFulltextAttach(options: FulltextAttachCommandOptions): Promise<FulltextAttachResult>;
+//# sourceMappingURL=attach.d.ts.map

package/dist/cli/commands/fulltext/attach.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/commands/fulltext/attach.js

@@ -0,0 +1,67 @@
+import { readFile } from "node:fs/promises";
+import { join } from "node:path";
+import { refExport, refFulltextAttach } from "../../../integration/ref-cli.js";
+import { processFulltextEntries } from "../../../fulltext/attach-shared.js";
+async function buildRefLookupFromLibrary(libraryPath, refCliOptions) {
+  const lookup = /* @__PURE__ */ new Map();
+  try {
+    const content = await readFile(libraryPath, "utf-8");
+    const parsed = JSON.parse(content);
+    if (!Array.isArray(parsed)) {
+      console.warn("Warning: Reference library file is not a JSON array. Falling back to ref export.");
+      throw new Error("Not an array");
+    }
+    const entries = parsed;
+    for (const entry of entries) {
+      const id = entry["id"];
+      if (!id) continue;
+      const doi = entry["DOI"];
+      if (doi && typeof doi === "string") {
+        lookup.set(`doi:${doi}`, id);
+      }
+      const pmid = entry["PMID"];
+      if (pmid && typeof pmid === "string") {
+        lookup.set(`pmid:${pmid}`, id);
+      }
+    }
+  } catch {
+    try {
+      const entries = await refExport("*", refCliOptions);
+      if (Array.isArray(entries)) {
+        for (const entry of entries) {
+          const id = entry["id"];
+          if (!id) continue;
+          const doi = entry["DOI"];
+          if (doi && typeof doi === "string") {
+            lookup.set(`doi:${doi}`, id);
+          }
+          const pmid = entry["PMID"];
+          if (pmid && typeof pmid === "string") {
+            lookup.set(`pmid:${pmid}`, id);
+          }
+        }
+      }
+    } catch {
+      console.warn('Warning: Could not read reference library. All articles will be skipped as "not_in_ref".');
+    }
+  }
+  return lookup;
+}
+async function executeFulltextAttach(options) {
+  const { sessionDir, dryRun, onProgress } = options;
+  const fulltextDir = join(sessionDir, "fulltext");
+  const libraryPath = join(sessionDir, "references.json");
+  const refCliOptions = { libraryPath };
+  const refLookup = await buildRefLookupFromLibrary(libraryPath, refCliOptions);
+  return processFulltextEntries({
+    fulltextDir,
+    refLookup,
+    attachFile: (refId, filePath) => refFulltextAttach(refId, filePath, refCliOptions),
+    dryRun,
+    ...onProgress ? { onProgress } : {}
+  });
+}
+export {
+  executeFulltextAttach
+};
+//# sourceMappingURL=attach.js.map

package/dist/cli/commands/fulltext/attach.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"attach.js","sources":["../../../../src/cli/commands/fulltext/attach.ts"],"sourcesContent":["/**\n * Standalone fulltext attach command.\n * Attaches fulltext files to existing reference-manager entries.\n */\n\nimport { readFile } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport type { FulltextAttachResult } from '../../../integration/types.js';\nimport { refFulltextAttach, refExport, type RefCliOptions } from '../../../integration/ref-cli.js';\nimport { processFulltextEntries } from '../../../fulltext/attach-shared.js';\n\nexport interface FulltextAttachCommandOptions {\n  sessionDir: string;\n  dryRun: boolean;\n  onProgress?: (current: number, total: number) => void;\n}\n\n/**\n * Load the reference library and build a lookup map from identifiers to ref IDs.\n * Returns a map with keys like \"doi:10.1234/test\" and \"pmid:12345678\".\n */\nasync function buildRefLookupFromLibrary(\n  libraryPath: string,\n  refCliOptions: RefCliOptions,\n): Promise<Map<string, string>> {\n  const lookup = new Map<string, string>();\n\n  try {\n    // Try to read library directly from JSON file\n    const content = await readFile(libraryPath, 'utf-8');\n    const parsed: unknown = JSON.parse(content);\n\n    if (!Array.isArray(parsed)) {\n      console.warn('Warning: Reference library file is not a JSON array. Falling back to ref export.');\n      throw new Error('Not an array');\n    }\n\n    const entries = parsed as Array<Record<string, unknown>>;\n    for (const entry of entries) {\n      const id = entry['id'] as string;\n      if (!id) continue;\n\n      const doi = entry['DOI'];\n      if (doi && typeof doi === 'string') {\n        lookup.set(`doi:${doi}`, id);\n      }\n      const pmid = entry['PMID'];\n      if (pmid && typeof pmid === 'string') {\n        lookup.set(`pmid:${pmid}`, id);\n      }\n    }\n  } catch {\n    // If library doesn't exist or can't be read, try ref export\n    try {\n      const entries = await refExport('*', refCliOptions) as Array<Record<string, unknown>>;\n      if (Array.isArray(entries)) {\n        for (const entry of entries) {\n          const id = entry['id'] as string;\n          if (!id) continue;\n          const doi = entry['DOI'];\n          if (doi && typeof doi === 'string') {\n            lookup.set(`doi:${doi}`, id);\n          }\n          const pmid = entry['PMID'];\n          if (pmid && typeof pmid === 'string') {\n            lookup.set(`pmid:${pmid}`, id);\n          }\n        }\n      }\n    } catch {\n      console.warn('Warning: Could not read reference library. All articles will be skipped as \"not_in_ref\".');\n    }\n  }\n\n  return lookup;\n}\n\n/**\n * Execute the standalone fulltext attach command.\n * Reads the session's fulltext directories and attaches files to ref entries.\n */\nexport async function executeFulltextAttach(\n  options: FulltextAttachCommandOptions,\n): Promise<FulltextAttachResult> {\n  const { sessionDir, dryRun, onProgress } = options;\n  const fulltextDir = join(sessionDir, 'fulltext');\n  const libraryPath = join(sessionDir, 'references.json');\n  const refCliOptions: RefCliOptions = { libraryPath };\n\n  // Build ref lookup from library\n  const refLookup = await buildRefLookupFromLibrary(libraryPath, refCliOptions);\n\n  return processFulltextEntries({\n    fulltextDir,\n    refLookup,\n    attachFile: (refId, filePath) => refFulltextAttach(refId, filePath, refCliOptions),\n    dryRun,\n    ...(onProgress ? { onProgress } : {}),\n  });\n}\n"],"names":[],"mappings":";;;;AAqBA,eAAe,0BACb,aACA,eAC8B;AAC9B,QAAM,6BAAa,IAAA;AAEnB,MAAI;AAEF,UAAM,UAAU,MAAM,SAAS,aAAa,OAAO;AACnD,UAAM,SAAkB,KAAK,MAAM,OAAO;AAE1C,QAAI,CAAC,MAAM,QAAQ,MAAM,GAAG;AAC1B,cAAQ,KAAK,kFAAkF;AAC/F,YAAM,IAAI,MAAM,cAAc;AAAA,IAChC;AAEA,UAAM,UAAU;AAChB,eAAW,SAAS,SAAS;AAC3B,YAAM,KAAK,MAAM,IAAI;AACrB,UAAI,CAAC,GAAI;AAET,YAAM,MAAM,MAAM,KAAK;AACvB,UAAI,OAAO,OAAO,QAAQ,UAAU;AAClC,eAAO,IAAI,OAAO,GAAG,IAAI,EAAE;AAAA,MAC7B;AACA,YAAM,OAAO,MAAM,MAAM;AACzB,UAAI,QAAQ,OAAO,SAAS,UAAU;AACpC,eAAO,IAAI,QAAQ,IAAI,IAAI,EAAE;AAAA,MAC/B;AAAA,IACF;AAAA,EACF,QAAQ;AAEN,QAAI;AACF,YAAM,UAAU,MAAM,UAAU,KAAK,aAAa;AAClD,UAAI,MAAM,QAAQ,OAAO,GAAG;AAC1B,mBAAW,SAAS,SAAS;AAC3B,gBAAM,KAAK,MAAM,IAAI;AACrB,cAAI,CAAC,GAAI;AACT,gBAAM,MAAM,MAAM,KAAK;AACvB,cAAI,OAAO,OAAO,QAAQ,UAAU;AAClC,mBAAO,IAAI,OAAO,GAAG,IAAI,EAAE;AAAA,UAC7B;AACA,gBAAM,OAAO,MAAM,MAAM;AACzB,cAAI,QAAQ,OAAO,SAAS,UAAU;AACpC,mBAAO,IAAI,QAAQ,IAAI,IAAI,EAAE;AAAA,UAC/B;AAAA,QACF;AAAA,MACF;AAAA,IACF,QAAQ;AACN,cAAQ,KAAK,0FAA0F;AAAA,IACzG;AAAA,EACF;AAEA,SAAO;AACT;AAMA,eAAsB,sBACpB,SAC+B;AAC/B,QAAM,EAAE,YAAY,QAAQ,WAAA,IAAe;AAC3C,QAAM,cAAc,KAAK,YAAY,UAAU;AAC/C,QAAM,cAAc,KAAK,YAAY,iBAAiB;AACtD,QAAM,gBAA+B,EAAE,YAAA;AAGvC,QAAM,YAAY,MAAM,0BAA0B,aAAa,aAAa;AAE5E,SAAO,uBAAuB;AAAA,IAC5B;AAAA,IACA;AAAA,IACA,YAAY,CAAC,OAAO,aAAa,kBAAkB,OAAO,UAAU,aAAa;AAAA,IACjF;AAAA,IACA,GAAI,aAAa,EAAE,eAAe,CAAA;AAAA,EAAC,CACpC;AACH;"}

package/dist/cli/commands/fulltext/check.d.ts

@@ -0,0 +1,30 @@
+import { DiscoveryConfig } from '../../../fulltext/discovery/index';
+import { OAStatus } from '../../../fulltext/types';
+export interface FulltextCheckOptions {
+    sessionDir: string;
+    config: DiscoveryConfig;
+    concurrency?: number;
+}
+export interface FulltextCheckArticleResult {
+    doi?: string;
+    pmid?: string;
+    title: string;
+    oaStatus: OAStatus;
+    locationCount: number;
+}
+export interface FulltextCheckResult {
+    summary: {
+        total: number;
+        open: number;
+        closed: number;
+        unknown: number;
+    };
+    articles: FulltextCheckArticleResult[];
+}
+/**
+ * Execute the fulltext check command.
+ * Checks OA availability for all included articles in a session,
+ * processing articles in parallel with a concurrency limit.
+ */
+export declare function executeFulltextCheck(options: FulltextCheckOptions): Promise<FulltextCheckResult>;
+//# sourceMappingURL=check.d.ts.map

package/dist/cli/commands/fulltext/check.d.ts.map

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package/dist/cli/commands/fulltext/check.js

@@ -0,0 +1,113 @@
+import { readFile, access, readdir } from "node:fs/promises";
+import { join } from "node:path";
+import { parse } from "yaml";
+import { discoverOA } from "../../../fulltext/discovery/index.js";
+import { loadMeta, saveMeta } from "../../../fulltext/meta.js";
+const DEFAULT_CONCURRENCY = 3;
+async function loadIncludedArticles(sessionDir) {
+  const reviewsPath = join(sessionDir, ".internal", "reviews.yaml");
+  const content = await readFile(reviewsPath, "utf-8");
+  const reviewFile = parse(content);
+  return reviewFile.articles.filter((a) => a.finalDecision === "include");
+}
+async function findArticleDir(sessionDir, article) {
+  const fulltextDir = join(sessionDir, "fulltext");
+  try {
+    await access(fulltextDir);
+  } catch {
+    return null;
+  }
+  let entries;
+  try {
+    const dirEntries = await readdir(fulltextDir);
+    entries = dirEntries.map(String);
+  } catch {
+    return null;
+  }
+  for (const entry of entries) {
+    try {
+      const metaPath = join(fulltextDir, entry, "meta.json");
+      const meta = await loadMeta(metaPath);
+      if (article.doi && meta.doi === article.doi) return entry;
+      if (article.pmid && meta.pmid === article.pmid) return entry;
+    } catch {
+    }
+  }
+  return null;
+}
+async function processArticle(article, sessionDir, config) {
+  const discoveryArticle = {};
+  if (article.doi) discoveryArticle.doi = article.doi;
+  if (article.pmid) discoveryArticle.pmid = article.pmid;
+  if (article.arxivId) discoveryArticle.arxivId = article.arxivId;
+  const discoveryResult = await discoverOA(discoveryArticle, config);
+  const articleResult = {
+    title: article.title,
+    oaStatus: discoveryResult.oaStatus,
+    locationCount: discoveryResult.locations.length
+  };
+  if (article.doi) articleResult.doi = article.doi;
+  if (article.pmid) articleResult.pmid = article.pmid;
+  const dirName = await findArticleDir(sessionDir, article);
+  if (dirName) {
+    try {
+      const metaPath = join(sessionDir, "fulltext", dirName, "meta.json");
+      const meta = await loadMeta(metaPath);
+      meta.oaStatus = discoveryResult.oaStatus;
+      meta.oaLocations = discoveryResult.locations;
+      meta.checkedAt = (/* @__PURE__ */ new Date()).toISOString();
+      await saveMeta(metaPath, meta);
+    } catch {
+    }
+  }
+  return articleResult;
+}
+async function runWithConcurrency(tasks, concurrency) {
+  const results = new Array(tasks.length);
+  let nextIndex = 0;
+  async function worker() {
+    while (nextIndex < tasks.length) {
+      const index = nextIndex++;
+      try {
+        const value = await tasks[index]();
+        results[index] = { status: "fulfilled", value };
+      } catch (reason) {
+        results[index] = { status: "rejected", reason };
+      }
+    }
+  }
+  const workers = Array.from({ length: Math.min(concurrency, tasks.length) }, () => worker());
+  await Promise.all(workers);
+  return results;
+}
+async function executeFulltextCheck(options) {
+  const { sessionDir, config, concurrency = DEFAULT_CONCURRENCY } = options;
+  const articles = await loadIncludedArticles(sessionDir);
+  const summary = { total: articles.length, open: 0, closed: 0, unknown: 0 };
+  const tasks = articles.map(
+    (article) => () => processArticle(article, sessionDir, config)
+  );
+  const settled = await runWithConcurrency(tasks, concurrency);
+  const results = [];
+  for (const result of settled) {
+    if (result.status === "fulfilled") {
+      results.push(result.value);
+      switch (result.value.oaStatus) {
+        case "open":
+          summary.open++;
+          break;
+        case "closed":
+          summary.closed++;
+          break;
+        case "unknown":
+          summary.unknown++;
+          break;
+      }
+    }
+  }
+  return { summary, articles: results };
+}
+export {
+  executeFulltextCheck
+};
+//# sourceMappingURL=check.js.map

package/dist/cli/commands/fulltext/check.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"check.js","sources":["../../../../src/cli/commands/fulltext/check.ts"],"sourcesContent":["/**\n * Fulltext check command.\n * Checks OA availability for included articles in a session.\n */\n\nimport { readFile, readdir, access } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { parse as parseYaml } from 'yaml';\nimport { discoverOA, type DiscoveryConfig, type DiscoveryArticle } from '../../../fulltext/discovery/index';\nimport { loadMeta, saveMeta } from '../../../fulltext/meta';\nimport type { OAStatus } from '../../../fulltext/types';\nimport type { ReviewFile, ArticleEntry } from '../review/types';\n\n/** Default concurrency for parallel article processing */\nconst DEFAULT_CONCURRENCY = 3;\n\nexport interface FulltextCheckOptions {\n  sessionDir: string;\n  config: DiscoveryConfig;\n  concurrency?: number;\n}\n\nexport interface FulltextCheckArticleResult {\n  doi?: string;\n  pmid?: string;\n  title: string;\n  oaStatus: OAStatus;\n  locationCount: number;\n}\n\nexport interface FulltextCheckResult {\n  summary: {\n    total: number;\n    open: number;\n    closed: number;\n    unknown: number;\n  };\n  articles: FulltextCheckArticleResult[];\n}\n\n/**\n * Load included articles from reviews.yaml\n */\nasync function loadIncludedArticles(sessionDir: string): Promise<ArticleEntry[]> {\n  const reviewsPath = join(sessionDir, '.internal', 'reviews.yaml');\n  const content = await readFile(reviewsPath, 'utf-8');\n  const reviewFile = parseYaml(content) as ReviewFile;\n  return reviewFile.articles.filter((a) => a.finalDecision === 'include');\n}\n\n/**\n * Try to find a meta.json matching an article in the fulltext directory.\n * Returns the dirName if found, null otherwise.\n */\nasync function findArticleDir(\n  sessionDir: string,\n  article: ArticleEntry\n): Promise<string | null> {\n  const fulltextDir = join(sessionDir, 'fulltext');\n  try {\n    await access(fulltextDir);\n  } catch {\n    return null;\n  }\n\n  let entries: string[];\n  try {\n    const dirEntries = await readdir(fulltextDir);\n    entries = dirEntries.map(String);\n  } catch {\n    return null;\n  }\n\n  for (const entry of entries) {\n    try {\n      const metaPath = join(fulltextDir, entry, 'meta.json');\n      const meta = await loadMeta(metaPath);\n      // Match by DOI or PMID\n      if (article.doi && meta.doi === article.doi) return entry;\n      if (article.pmid && meta.pmid === article.pmid) return entry;\n    } catch {\n      // Skip entries without valid meta.json\n    }\n  }\n  return null;\n}\n\n/**\n * Process a single article: run OA discovery and optionally update meta.json.\n */\nasync function processArticle(\n  article: ArticleEntry,\n  sessionDir: string,\n  config: DiscoveryConfig\n): Promise<FulltextCheckArticleResult> {\n  const discoveryArticle: DiscoveryArticle = {};\n  if (article.doi) discoveryArticle.doi = article.doi;\n  if (article.pmid) discoveryArticle.pmid = article.pmid;\n  if (article.arxivId) discoveryArticle.arxivId = article.arxivId;\n  const discoveryResult = await discoverOA(discoveryArticle, config);\n\n  const articleResult: FulltextCheckArticleResult = {\n    title: article.title,\n    oaStatus: discoveryResult.oaStatus,\n    locationCount: discoveryResult.locations.length,\n  };\n  if (article.doi) articleResult.doi = article.doi;\n  if (article.pmid) articleResult.pmid = article.pmid;\n\n  // Try to update meta.json if a fulltext directory exists for this article\n  const dirName = await findArticleDir(sessionDir, article);\n  if (dirName) {\n    try {\n      const metaPath = join(sessionDir, 'fulltext', dirName, 'meta.json');\n      const meta = await loadMeta(metaPath);\n      meta.oaStatus = discoveryResult.oaStatus;\n      meta.oaLocations = discoveryResult.locations;\n      meta.checkedAt = new Date().toISOString();\n      await saveMeta(metaPath, meta);\n    } catch {\n      // Meta update is best-effort\n    }\n  }\n\n  return articleResult;\n}\n\n/**\n * Run async tasks with a concurrency limit.\n */\nasync function runWithConcurrency<T>(\n  tasks: Array<() => Promise<T>>,\n  concurrency: number\n): Promise<PromiseSettledResult<T>[]> {\n  const results: PromiseSettledResult<T>[] = new Array(tasks.length);\n  let nextIndex = 0;\n\n  async function worker(): Promise<void> {\n    while (nextIndex < tasks.length) {\n      const index = nextIndex++;\n      try {\n        const value = await tasks[index]!();\n        results[index] = { status: 'fulfilled', value };\n      } catch (reason) {\n        results[index] = { status: 'rejected', reason };\n      }\n    }\n  }\n\n  const workers = Array.from({ length: Math.min(concurrency, tasks.length) }, () => worker());\n  await Promise.all(workers);\n  return results;\n}\n\n/**\n * Execute the fulltext check command.\n * Checks OA availability for all included articles in a session,\n * processing articles in parallel with a concurrency limit.\n */\nexport async function executeFulltextCheck(\n  options: FulltextCheckOptions\n): Promise<FulltextCheckResult> {\n  const { sessionDir, config, concurrency = DEFAULT_CONCURRENCY } = options;\n\n  // Load included articles\n  const articles = await loadIncludedArticles(sessionDir);\n\n  const summary = { total: articles.length, open: 0, closed: 0, unknown: 0 };\n\n  const tasks = articles.map(\n    (article) => () => processArticle(article, sessionDir, config)\n  );\n\n  const settled = await runWithConcurrency(tasks, concurrency);\n\n  const results: FulltextCheckArticleResult[] = [];\n  for (const result of settled) {\n    if (result.status === 'fulfilled') {\n      results.push(result.value);\n      switch (result.value.oaStatus) {\n        case 'open':\n          summary.open++;\n          break;\n        case 'closed':\n          summary.closed++;\n          break;\n        case 'unknown':\n          summary.unknown++;\n          break;\n      }\n    }\n  }\n\n  return { summary, articles: results 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package/dist/cli/commands/fulltext/convert.d.ts

@@ -0,0 +1,22 @@
+/**
+ * Fulltext convert command - converts PMC XML to Markdown.
+ */
+export interface FulltextConvertOptions {
+    sessionId: string;
+    article?: string;
+}
+export interface ConvertArticleResult {
+    dirName: string;
+    title: string;
+    status: 'converted' | 'skipped' | 'failed';
+    error?: string;
+}
+export interface ConvertCommandResult {
+    success: boolean;
+    converted: number;
+    skipped: number;
+    failed: number;
+    articles: ConvertArticleResult[];
+}
+export declare function executeFulltextConvert(options: FulltextConvertOptions, sessionsDir: string): Promise<ConvertCommandResult>;
+//# sourceMappingURL=convert.d.ts.map

package/dist/cli/commands/fulltext/convert.d.ts.map

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package/dist/cli/commands/fulltext/convert.js

@@ -0,0 +1,84 @@
+import { readdir, stat } from "node:fs/promises";
+import { join } from "node:path";
+import { getArticleDir, getMetaPath, getFulltextDir } from "../../../fulltext/paths.js";
+import { convertPmcXmlToMarkdown } from "../../../fulltext/convert/index.js";
+async function fileExists(path) {
+  try {
+    await stat(path);
+    return true;
+  } catch {
+    return false;
+  }
+}
+async function getArticleDirs(sessionDir, articleFilter) {
+  const fulltextDir = getFulltextDir(sessionDir);
+  if (articleFilter) {
+    const articlePath = getArticleDir(sessionDir, articleFilter);
+    if (await fileExists(articlePath)) {
+      return [articleFilter];
+    }
+    return [];
+  }
+  try {
+    const entries = await readdir(fulltextDir, { withFileTypes: true });
+    return entries.filter((e) => e.isDirectory()).map((e) => e.name);
+  } catch {
+    return [];
+  }
+}
+async function executeFulltextConvert(options, sessionsDir) {
+  const sessionDir = join(sessionsDir, options.sessionId);
+  const articleDirs = await getArticleDirs(sessionDir, options.article);
+  const articles = [];
+  let converted = 0;
+  let skipped = 0;
+  let failed = 0;
+  for (const dirName of articleDirs) {
+    const articleDir = getArticleDir(sessionDir, dirName);
+    const xmlPath = join(articleDir, "fulltext.xml");
+    const mdPath = join(articleDir, "fulltext.md");
+    const metaPath = getMetaPath(sessionDir, dirName);
+    if (!await fileExists(xmlPath)) {
+      continue;
+    }
+    if (await fileExists(mdPath)) {
+      skipped++;
+      articles.push({ dirName, title: dirName, status: "skipped" });
+      continue;
+    }
+    const metaPathExists = await fileExists(metaPath);
+    const result = await convertPmcXmlToMarkdown(
+      xmlPath,
+      mdPath,
+      metaPathExists ? metaPath : void 0
+    );
+    if (result.success) {
+      converted++;
+      articles.push({
+        dirName,
+        title: result.title ?? dirName,
+        status: "converted"
+      });
+    } else {
+      failed++;
+      const articleResult = {
+        dirName,
+        title: dirName,
+        status: "failed"
+      };
+      if (result.error) articleResult.error = result.error;
+      articles.push(articleResult);
+    }
+  }
+  return {
+    success: failed === 0,
+    converted,
+    skipped,
+    failed,
+    articles
+  };
+}
+export {
+  executeFulltextConvert
+};
+//# sourceMappingURL=convert.js.map

package/dist/cli/commands/fulltext/convert.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"convert.js","sources":["../../../../src/cli/commands/fulltext/convert.ts"],"sourcesContent":["/**\n * Fulltext convert command - converts PMC XML to Markdown.\n */\n\nimport { readdir, stat } from 'node:fs/promises';\nimport { join } from 'node:path';\nimport { getFulltextDir, getArticleDir, getMetaPath } from '../../../fulltext/paths.js';\nimport { convertPmcXmlToMarkdown } from '../../../fulltext/convert/index.js';\n\nexport interface FulltextConvertOptions {\n  sessionId: string;\n  article?: string;\n}\n\nexport interface ConvertArticleResult {\n  dirName: string;\n  title: string;\n  status: 'converted' | 'skipped' | 'failed';\n  error?: string;\n}\n\nexport interface ConvertCommandResult {\n  success: boolean;\n  converted: number;\n  skipped: number;\n  failed: number;\n  articles: ConvertArticleResult[];\n}\n\nasync function fileExists(path: string): Promise<boolean> {\n  try {\n    await stat(path);\n    return true;\n  } catch {\n    return false;\n  }\n}\n\n/**\n * Get list of article directory names to process.\n */\nasync function getArticleDirs(\n  sessionDir: string,\n  articleFilter?: string,\n): Promise<string[]> {\n  const fulltextDir = getFulltextDir(sessionDir);\n\n  if (articleFilter) {\n    // Filter to specific article\n    const articlePath = getArticleDir(sessionDir, articleFilter);\n    if (await fileExists(articlePath)) {\n      return [articleFilter];\n    }\n    return [];\n  }\n\n  // List all directories in fulltext/\n  try {\n    const entries = await readdir(fulltextDir, { withFileTypes: true });\n    return entries\n      .filter((e) => e.isDirectory())\n      .map((e) => e.name);\n  } catch {\n    return [];\n  }\n}\n\nexport async function executeFulltextConvert(\n  options: FulltextConvertOptions,\n  sessionsDir: string,\n): Promise<ConvertCommandResult> {\n  const sessionDir = join(sessionsDir, options.sessionId);\n  const articleDirs = await getArticleDirs(sessionDir, options.article);\n\n  const articles: ConvertArticleResult[] = [];\n  let converted = 0;\n  let skipped = 0;\n  let failed = 0;\n\n  for (const dirName of articleDirs) {\n    const articleDir = getArticleDir(sessionDir, dirName);\n    const xmlPath = join(articleDir, 'fulltext.xml');\n    const mdPath = join(articleDir, 'fulltext.md');\n    const metaPath = getMetaPath(sessionDir, dirName);\n\n    // Check if XML exists\n    if (!(await fileExists(xmlPath))) {\n      continue; // No XML to convert, skip silently\n    }\n\n    // Check if already converted\n    if (await fileExists(mdPath)) {\n      skipped++;\n      articles.push({ dirName, title: dirName, status: 'skipped' });\n      continue;\n    }\n\n    // Convert\n    const metaPathExists = await fileExists(metaPath);\n    const result = await convertPmcXmlToMarkdown(\n      xmlPath,\n      mdPath,\n      metaPathExists ? metaPath : undefined,\n    );\n\n    if (result.success) {\n      converted++;\n      articles.push({\n        dirName,\n        title: result.title ?? dirName,\n        status: 'converted',\n      });\n    } else {\n      failed++;\n      const articleResult: ConvertArticleResult = {\n        dirName,\n        title: dirName,\n        status: 'failed',\n      };\n      if (result.error) articleResult.error = result.error;\n      articles.push(articleResult);\n    }\n  }\n\n  return {\n    success: failed === 0,\n    converted,\n    skipped,\n    failed,\n    articles,\n  };\n}\n"],"names":[],"mappings":";;;;AA6BA,eAAe,WAAW,MAAgC;AACxD,MAAI;AACF,UAAM,KAAK,IAAI;AACf,WAAO;AAAA,EACT,QAAQ;AACN,WAAO;AAAA,EACT;AACF;AAKA,eAAe,eACb,YACA,eACmB;AACnB,QAAM,cAAc,eAAe,UAAU;AAE7C,MAAI,eAAe;AAEjB,UAAM,cAAc,cAAc,YAAY,aAAa;AAC3D,QAAI,MAAM,WAAW,WAAW,GAAG;AACjC,aAAO,CAAC,aAAa;AAAA,IACvB;AACA,WAAO,CAAA;AAAA,EACT;AAGA,MAAI;AACF,UAAM,UAAU,MAAM,QAAQ,aAAa,EAAE,eAAe,MAAM;AAClE,WAAO,QACJ,OAAO,CAAC,MAAM,EAAE,aAAa,EAC7B,IAAI,CAAC,MAAM,EAAE,IAAI;AAAA,EACtB,QAAQ;AACN,WAAO,CAAA;AAAA,EACT;AACF;AAEA,eAAsB,uBACpB,SACA,aAC+B;AAC/B,QAAM,aAAa,KAAK,aAAa,QAAQ,SAAS;AACtD,QAAM,cAAc,MAAM,eAAe,YAAY,QAAQ,OAAO;AAEpE,QAAM,WAAmC,CAAA;AACzC,MAAI,YAAY;AAChB,MAAI,UAAU;AACd,MAAI,SAAS;AAEb,aAAW,WAAW,aAAa;AACjC,UAAM,aAAa,cAAc,YAAY,OAAO;AACpD,UAAM,UAAU,KAAK,YAAY,cAAc;AAC/C,UAAM,SAAS,KAAK,YAAY,aAAa;AAC7C,UAAM,WAAW,YAAY,YAAY,OAAO;AAGhD,QAAI,CAAE,MAAM,WAAW,OAAO,GAAI;AAChC;AAAA,IACF;AAGA,QAAI,MAAM,WAAW,MAAM,GAAG;AAC5B;AACA,eAAS,KAAK,EAAE,SAAS,OAAO,SAAS,QAAQ,WAAW;AAC5D;AAAA,IACF;AAGA,UAAM,iBAAiB,MAAM,WAAW,QAAQ;AAChD,UAAM,SAAS,MAAM;AAAA,MACnB;AAAA,MACA;AAAA,MACA,iBAAiB,WAAW;AAAA,IAAA;AAG9B,QAAI,OAAO,SAAS;AAClB;AACA,eAAS,KAAK;AAAA,QACZ;AAAA,QACA,OAAO,OAAO,SAAS;AAAA,QACvB,QAAQ;AAAA,MAAA,CACT;AAAA,IACH,OAAO;AACL;AACA,YAAM,gBAAsC;AAAA,QAC1C;AAAA,QACA,OAAO;AAAA,QACP,QAAQ;AAAA,MAAA;AAEV,UAAI,OAAO,MAAO,eAAc,QAAQ,OAAO;AAC/C,eAAS,KAAK,aAAa;AAAA,IAC7B;AAAA,EACF;AAEA,SAAO;AAAA,IACL,SAAS,WAAW;AAAA,IACpB;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EAAA;AAEJ;"}

package/dist/cli/commands/fulltext/fetch.d.ts

@@ -0,0 +1,35 @@
+/**
+ * Fulltext fetch command - downloads OA fulltexts for session articles.
+ */
+export interface FulltextFetchOptions {
+    sessionId: string;
+    sessionsDir: string;
+    source?: string[];
+    convertMarkdown?: boolean;
+    dryRun?: boolean;
+    concurrency?: number;
+    retryDelay?: number;
+}
+export interface FulltextFetchArticle {
+    dirName: string;
+    title: string;
+    oaStatus: string;
+    locationCount: number;
+}
+export interface FulltextFetchResult {
+    summary: {
+        total: number;
+        downloaded: number;
+        failed: number;
+        skipped: number;
+    };
+    articles: FulltextFetchArticle[];
+    dryRun?: boolean;
+}
+/**
+ * Execute the fulltext fetch command.
+ * Loads articles from reviews.yaml, checks OA status via meta.json,
+ * and downloads PDFs/XMLs from OA sources.
+ */
+export declare function executeFulltextFetch(options: FulltextFetchOptions): Promise<FulltextFetchResult>;
+//# sourceMappingURL=fetch.d.ts.map

package/dist/cli/commands/fulltext/fetch.d.ts.map

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