@ncukondo/search-hub 0.23.1 → 0.24.0

package/dist/cli/utils/argv.d.ts

@@ -0,0 +1,34 @@
+import { Command } from 'commander';
+/**
+ * Extract the subcommand name from argv (best-effort).
+ *
+ * Skips global options that take a value so things like `--config upgrade`
+ * are not misread as the `upgrade` subcommand. The set of value-taking
+ * options is derived from the Commander program itself, so it stays in sync
+ * with the option definitions.
+ */
+export declare function extractCommandName(argv: string[], program: Command): string;
+/**
+ * Best-effort detection of `--no-update-check` in argv, without relying on
+ * Commander having parsed yet (the async check starts before parseAsync).
+ */
+export declare function hasNoUpdateCheckFlag(argv: string[]): boolean;
+/**
+ * Best-effort detection of the global `--quiet` flag in argv, without relying
+ * on Commander having parsed yet (the async check starts before parseAsync).
+ * `--quiet` promises "suppress all output except errors", which includes the
+ * update notice.
+ */
+export declare function hasQuietFlag(argv: string[]): boolean;
+/**
+ * Rewrite `search-hub upgrade --version <tag>` to `--version=<tag>`.
+ *
+ * The program has `.version(VERSION)` which registers a no-arg `--version`
+ * flag at the root. Commander's parser consumes the root `--version` before
+ * subcommand options, so the space-separated form is caught by the root
+ * (prints + exits) instead of reaching `upgrade`'s `--version <tag>`. The
+ * `=` form binds the value to the subcommand's option and sidesteps the
+ * root flag.
+ */
+export declare function rewriteUpgradeVersionFlag(argv: string[], program: Command): string[];
+//# sourceMappingURL=argv.d.ts.map

package/dist/cli/utils/argv.d.ts.map

@@ -0,0 +1 @@
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package/dist/cli/utils/argv.js

@@ -0,0 +1,63 @@
+function collectValueTakingFlags(program) {
+  const flags = /* @__PURE__ */ new Set();
+  for (const opt of program.options) {
+    if (!opt.required && !opt.optional) continue;
+    if (opt.long) flags.add(opt.long);
+    if (opt.short) flags.add(opt.short);
+  }
+  return flags;
+}
+function extractCommandName(argv, program) {
+  const valueTakingFlags = collectValueTakingFlags(program);
+  let skipNext = false;
+  for (let i = 2; i < argv.length; i++) {
+    const token = argv[i];
+    if (!token) continue;
+    if (skipNext) {
+      skipNext = false;
+      continue;
+    }
+    if (token.startsWith("-")) {
+      if (!token.includes("=") && valueTakingFlags.has(token)) skipNext = true;
+      continue;
+    }
+    return token;
+  }
+  return "";
+}
+function hasNoUpdateCheckFlag(argv) {
+  for (let i = 2; i < argv.length; i++) {
+    if (argv[i] === "--no-update-check") return true;
+  }
+  return false;
+}
+function hasQuietFlag(argv) {
+  for (let i = 2; i < argv.length; i++) {
+    if (argv[i] === "--quiet") return true;
+  }
+  return false;
+}
+function rewriteUpgradeVersionFlag(argv, program) {
+  if (extractCommandName(argv, program) !== "upgrade") return argv;
+  const out = [];
+  for (let i = 0; i < argv.length; i++) {
+    const token = argv[i];
+    if (token === "--version" && i + 1 < argv.length) {
+      const next = argv[i + 1];
+      if (next !== void 0 && !next.startsWith("-")) {
+        out.push(`--version=${next}`);
+        i++;
+        continue;
+      }
+    }
+    if (token !== void 0) out.push(token);
+  }
+  return out;
+}
+export {
+  extractCommandName,
+  hasNoUpdateCheckFlag,
+  hasQuietFlag,
+  rewriteUpgradeVersionFlag
+};
+//# sourceMappingURL=argv.js.map

package/dist/cli/utils/argv.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"argv.js","sources":["../../../src/cli/utils/argv.ts"],"sourcesContent":["/**\n * Argv helpers for the update-check notifier and the `upgrade` command.\n *\n * These run before Commander parses argv (the async update check starts\n * before command dispatch), so they are best-effort token scanners.\n */\nimport type { Command } from 'commander';\n\n/**\n * Collect flags (both `--long` and `-s`) for global options that take a value.\n * Used by {@link extractCommandName} so the subcommand parser can skip the\n * value after options like `--config <path>`.\n */\nfunction collectValueTakingFlags(program: Command): Set<string> {\n  const flags = new Set<string>();\n  for (const opt of program.options) {\n    if (!opt.required && !opt.optional) continue;\n    if (opt.long) flags.add(opt.long);\n    if (opt.short) flags.add(opt.short);\n  }\n  return flags;\n}\n\n/**\n * Extract the subcommand name from argv (best-effort).\n *\n * Skips global options that take a value so things like `--config upgrade`\n * are not misread as the `upgrade` subcommand. The set of value-taking\n * options is derived from the Commander program itself, so it stays in sync\n * with the option definitions.\n */\nexport function extractCommandName(argv: string[], program: Command): string {\n  const valueTakingFlags = collectValueTakingFlags(program);\n  let skipNext = false;\n  for (let i = 2; i < argv.length; i++) {\n    const token = argv[i];\n    if (!token) continue;\n    if (skipNext) {\n      skipNext = false;\n      continue;\n    }\n    if (token.startsWith('-')) {\n      // `--opt=value` bundles its value, no skip needed.\n      if (!token.includes('=') && valueTakingFlags.has(token)) skipNext = true;\n      continue;\n    }\n    return token;\n  }\n  return '';\n}\n\n/**\n * Best-effort detection of `--no-update-check` in argv, without relying on\n * Commander having parsed yet (the async check starts before parseAsync).\n */\nexport function hasNoUpdateCheckFlag(argv: string[]): boolean {\n  for (let i = 2; i < argv.length; i++) {\n    if (argv[i] === '--no-update-check') return true;\n  }\n  return false;\n}\n\n/**\n * Best-effort detection of the global `--quiet` flag in argv, without relying\n * on Commander having parsed yet (the async check starts before parseAsync).\n * `--quiet` promises \"suppress all output except errors\", which includes the\n * update notice.\n */\nexport function hasQuietFlag(argv: string[]): boolean {\n  for (let i = 2; i < argv.length; i++) {\n    if (argv[i] === '--quiet') return true;\n  }\n  return false;\n}\n\n/**\n * Rewrite `search-hub upgrade --version <tag>` to `--version=<tag>`.\n *\n * The program has `.version(VERSION)` which registers a no-arg `--version`\n * flag at the root. Commander's parser consumes the root `--version` before\n * subcommand options, so the space-separated form is caught by the root\n * (prints + exits) instead of reaching `upgrade`'s `--version <tag>`. The\n * `=` form binds the value to the subcommand's option and sidesteps the\n * root flag.\n */\nexport function rewriteUpgradeVersionFlag(argv: string[], program: Command): string[] {\n  if (extractCommandName(argv, program) !== 'upgrade') return argv;\n\n  const out: string[] = [];\n  for (let i = 0; i < argv.length; i++) {\n    const token = argv[i];\n    if (token === '--version' && i + 1 < argv.length) {\n      const next = argv[i + 1];\n      if (next !== undefined && !next.startsWith('-')) {\n        out.push(`--version=${next}`);\n        i++;\n        continue;\n      }\n    }\n    if (token !== undefined) out.push(token);\n  }\n  return out;\n}\n"],"names":[],"mappings":"AAaA,SAAS,wBAAwB,SAA+B;AAC9D,QAAM,4BAAY,IAAA;AAClB,aAAW,OAAO,QAAQ,SAAS;AACjC,QAAI,CAAC,IAAI,YAAY,CAAC,IAAI,SAAU;AACpC,QAAI,IAAI,KAAM,OAAM,IAAI,IAAI,IAAI;AAChC,QAAI,IAAI,MAAO,OAAM,IAAI,IAAI,KAAK;AAAA,EACpC;AACA,SAAO;AACT;AAUO,SAAS,mBAAmB,MAAgB,SAA0B;AAC3E,QAAM,mBAAmB,wBAAwB,OAAO;AACxD,MAAI,WAAW;AACf,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,UAAM,QAAQ,KAAK,CAAC;AACpB,QAAI,CAAC,MAAO;AACZ,QAAI,UAAU;AACZ,iBAAW;AACX;AAAA,IACF;AACA,QAAI,MAAM,WAAW,GAAG,GAAG;AAEzB,UAAI,CAAC,MAAM,SAAS,GAAG,KAAK,iBAAiB,IAAI,KAAK,EAAG,YAAW;AACpE;AAAA,IACF;AACA,WAAO;AAAA,EACT;AACA,SAAO;AACT;AAMO,SAAS,qBAAqB,MAAyB;AAC5D,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,QAAI,KAAK,CAAC,MAAM,oBAAqB,QAAO;AAAA,EAC9C;AACA,SAAO;AACT;AAQO,SAAS,aAAa,MAAyB;AACpD,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,QAAI,KAAK,CAAC,MAAM,UAAW,QAAO;AAAA,EACpC;AACA,SAAO;AACT;AAYO,SAAS,0BAA0B,MAAgB,SAA4B;AACpF,MAAI,mBAAmB,MAAM,OAAO,MAAM,UAAW,QAAO;AAE5D,QAAM,MAAgB,CAAA;AACtB,WAAS,IAAI,GAAG,IAAI,KAAK,QAAQ,KAAK;AACpC,UAAM,QAAQ,KAAK,CAAC;AACpB,QAAI,UAAU,eAAe,IAAI,IAAI,KAAK,QAAQ;AAChD,YAAM,OAAO,KAAK,IAAI,CAAC;AACvB,UAAI,SAAS,UAAa,CAAC,KAAK,WAAW,GAAG,GAAG;AAC/C,YAAI,KAAK,aAAa,IAAI,EAAE;AAC5B;AACA;AAAA,MACF;AAAA,IACF;AACA,QAAI,UAAU,OAAW,KAAI,KAAK,KAAK;AAAA,EACzC;AACA,SAAO;AACT;"}

package/dist/config/paths.js

@@ -5,6 +5,9 @@ const paths = envPaths("search-hub", { suffix: "" });
 function getConfigDir() {
   return paths.config;
 }
+function getDataDir() {
+  return paths.data;
+}
 function getDefaultConfigPath() {
   return join(paths.config, "config.toml");
 }
@@ -34,6 +37,7 @@ async function isInsideProject(baseDir) {
 }
 export {
   getConfigDir,
+  getDataDir,
   getDefaultConfigPath,
   getDefaultSessionsDir,
   getLocalConfigPath,

package/dist/config/paths.js.map

@@ -1 +1 @@
-{"version":3,"file":"paths.js","sources":["../../src/config/paths.ts"],"sourcesContent":["/**\n * Platform-specific paths using XDG Base Directory spec on Linux,\n * ~/Library on macOS, and AppData on Windows.\n */\nimport envPaths from 'env-paths';\nimport { join } from 'node:path';\nimport { stat } from 'node:fs/promises';\n\n// Use empty suffix to get clean 'search-hub' directory names\nconst paths = envPaths('search-hub', { suffix: '' });\n\n/**\n * Get the config directory for search-hub.\n * - Linux: ~/.config/search-hub\n * - macOS: ~/Library/Preferences/search-hub\n * - Windows: %APPDATA%\\search-hub\\Config\n */\nexport function getConfigDir(): string {\n  return paths.config;\n}\n\n/**\n * Get the data directory for search-hub.\n * - Linux: ~/.local/share/search-hub\n * - macOS: ~/Library/Application Support/search-hub\n * - Windows: %LOCALAPPDATA%\\search-hub\\Data\n */\nexport function getDataDir(): string {\n  return paths.data;\n}\n\n/**\n * Get the default config file path.\n */\nexport function getDefaultConfigPath(): string {\n  return join(paths.config, 'config.toml');\n}\n\n/**\n * Get the default sessions directory.\n */\nexport function getDefaultSessionsDir(): string {\n  return join(paths.data, 'sessions');\n}\n\n/** Name of the project-local directory. */\nconst PROJECT_DIR_NAME = '.search-hub';\n\n/**\n * Get the project directory path (.search-hub/) relative to a base directory.\n * Defaults to cwd.\n */\nexport function getProjectDir(baseDir?: string): string {\n  return join(baseDir ?? process.cwd(), PROJECT_DIR_NAME);\n}\n\n/**\n * Get the local config file path (.search-hub/config.toml).\n */\nexport function getLocalConfigPath(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'config.toml');\n}\n\n/**\n * Get the local sessions directory (.search-hub/sessions/).\n */\nexport function getLocalSessionsDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'sessions');\n}\n\n/**\n * Get the local queries directory (.search-hub/queries/).\n */\nexport function getQueriesDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'queries');\n}\n\n/**\n * Check if the given directory (default: cwd) contains a .search-hub/ project directory.\n */\nexport async function isInsideProject(baseDir?: string): Promise<boolean> {\n  try {\n    const stats = await stat(getProjectDir(baseDir));\n    return stats.isDirectory();\n  } catch {\n    return false;\n  }\n}\n"],"names":[],"mappings":";;;AASA,MAAM,QAAQ,SAAS,cAAc,EAAE,QAAQ,IAAI;AAQ5C,SAAS,eAAuB;AACrC,SAAO,MAAM;AACf;AAeO,SAAS,uBAA+B;AAC7C,SAAO,KAAK,MAAM,QAAQ,aAAa;AACzC;AAKO,SAAS,wBAAgC;AAC9C,SAAO,KAAK,MAAM,MAAM,UAAU;AACpC;AAGA,MAAM,mBAAmB;AAMlB,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,WAAW,QAAQ,IAAA,GAAO,gBAAgB;AACxD;AAKO,SAAS,mBAAmB,SAA0B;AAC3D,SAAO,KAAK,cAAc,OAAO,GAAG,aAAa;AACnD;AAKO,SAAS,oBAAoB,SAA0B;AAC5D,SAAO,KAAK,cAAc,OAAO,GAAG,UAAU;AAChD;AAKO,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,cAAc,OAAO,GAAG,SAAS;AAC/C;AAKA,eAAsB,gBAAgB,SAAoC;AACxE,MAAI;AACF,UAAM,QAAQ,MAAM,KAAK,cAAc,OAAO,CAAC;AAC/C,WAAO,MAAM,YAAA;AAAA,EACf,QAAQ;AACN,WAAO;AAAA,EACT;AACF;"}
+{"version":3,"file":"paths.js","sources":["../../src/config/paths.ts"],"sourcesContent":["/**\n * Platform-specific paths using XDG Base Directory spec on Linux,\n * ~/Library on macOS, and AppData on Windows.\n */\nimport envPaths from 'env-paths';\nimport { join } from 'node:path';\nimport { stat } from 'node:fs/promises';\n\n// Use empty suffix to get clean 'search-hub' directory names\nconst paths = envPaths('search-hub', { suffix: '' });\n\n/**\n * Get the config directory for search-hub.\n * - Linux: ~/.config/search-hub\n * - macOS: ~/Library/Preferences/search-hub\n * - Windows: %APPDATA%\\search-hub\\Config\n */\nexport function getConfigDir(): string {\n  return paths.config;\n}\n\n/**\n * Get the data directory for search-hub.\n * - Linux: ~/.local/share/search-hub\n * - macOS: ~/Library/Application Support/search-hub\n * - Windows: %LOCALAPPDATA%\\search-hub\\Data\n */\nexport function getDataDir(): string {\n  return paths.data;\n}\n\n/**\n * Get the default config file path.\n */\nexport function getDefaultConfigPath(): string {\n  return join(paths.config, 'config.toml');\n}\n\n/**\n * Get the default sessions directory.\n */\nexport function getDefaultSessionsDir(): string {\n  return join(paths.data, 'sessions');\n}\n\n/** Name of the project-local directory. */\nconst PROJECT_DIR_NAME = '.search-hub';\n\n/**\n * Get the project directory path (.search-hub/) relative to a base directory.\n * Defaults to cwd.\n */\nexport function getProjectDir(baseDir?: string): string {\n  return join(baseDir ?? process.cwd(), PROJECT_DIR_NAME);\n}\n\n/**\n * Get the local config file path (.search-hub/config.toml).\n */\nexport function getLocalConfigPath(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'config.toml');\n}\n\n/**\n * Get the local sessions directory (.search-hub/sessions/).\n */\nexport function getLocalSessionsDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'sessions');\n}\n\n/**\n * Get the local queries directory (.search-hub/queries/).\n */\nexport function getQueriesDir(baseDir?: string): string {\n  return join(getProjectDir(baseDir), 'queries');\n}\n\n/**\n * Check if the given directory (default: cwd) contains a .search-hub/ project directory.\n */\nexport async function isInsideProject(baseDir?: string): Promise<boolean> {\n  try {\n    const stats = await stat(getProjectDir(baseDir));\n    return stats.isDirectory();\n  } catch {\n    return false;\n  }\n}\n"],"names":[],"mappings":";;;AASA,MAAM,QAAQ,SAAS,cAAc,EAAE,QAAQ,IAAI;AAQ5C,SAAS,eAAuB;AACrC,SAAO,MAAM;AACf;AAQO,SAAS,aAAqB;AACnC,SAAO,MAAM;AACf;AAKO,SAAS,uBAA+B;AAC7C,SAAO,KAAK,MAAM,QAAQ,aAAa;AACzC;AAKO,SAAS,wBAAgC;AAC9C,SAAO,KAAK,MAAM,MAAM,UAAU;AACpC;AAGA,MAAM,mBAAmB;AAMlB,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,WAAW,QAAQ,IAAA,GAAO,gBAAgB;AACxD;AAKO,SAAS,mBAAmB,SAA0B;AAC3D,SAAO,KAAK,cAAc,OAAO,GAAG,aAAa;AACnD;AAKO,SAAS,oBAAoB,SAA0B;AAC5D,SAAO,KAAK,cAAc,OAAO,GAAG,UAAU;AAChD;AAKO,SAAS,cAAc,SAA0B;AACtD,SAAO,KAAK,cAAc,OAAO,GAAG,SAAS;AAC/C;AAKA,eAAsB,gBAAgB,SAAoC;AACxE,MAAI;AACF,UAAM,QAAQ,MAAM,KAAK,cAAc,OAAO,CAAC;AAC/C,WAAO,MAAM,YAAA;AAAA,EACf,QAAQ;AACN,WAAO;AAAA,EACT;AACF;"}

package/dist/integration/csl-json.d.ts

@@ -10,6 +10,7 @@ export interface CslJsonItem {
     }>;
     DOI?: string;
     PMID?: string;
+    URL?: string;
     abstract?: string;
     issued?: {
         'date-parts': number[][];
@@ -18,6 +19,15 @@ export interface CslJsonItem {
     volume?: string;
     issue?: string;
     page?: string;
+    /**
+     * Alternative identifiers. Key names match what reference-manager reads:
+     * its duplicate detector and fulltext discovery use `custom.arxiv_id`.
+     */
+    custom?: {
+        arxiv_id?: string;
+        eric_id?: string;
+        scopus_id?: string;
+    };
 }
 /**
  * Generate a human-readable CSL ID from an article (author-year format).

package/dist/integration/csl-json.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"csl-json.d.ts","sourceRoot":"","sources":["../../src/integration/csl-json.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,4BAA4B,CAAC;AAE1D,+CAA+C;AAC/C,MAAM,WAAW,WAAW;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IAClD,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE;QAAE,YAAY,EAAE,MAAM,EAAE,EAAE,CAAA;KAAE,CAAC;IACtC,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;IACd;;;OAGG;IACH,MAAM,CAAC,EAAE;QACP,QAAQ,CAAC,EAAE,MAAM,CAAC;QAClB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,SAAS,CAAC,EAAE,MAAM,CAAC;KACpB,CAAC;CACH;AAED;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,GAAG,MAAM,CAStD;AAYD;;;;;;;GAOG;AACH,wBAAgB,cAAc,CAC5B,IAAI,EAAE,MAAM,GAAG,SAAS,GACvB,MAAM,EAAE,EAAE,GAAG,SAAS,CAOxB;AAED;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,MAAM,GAAG,WAAW,CAyC1E;AAED;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,OAAO,EAAE,GAAG,WAAW,EAAE,CAqBpE"}

package/dist/integration/csl-json.js

@@ -27,6 +27,18 @@ function articleToCslJson(article, id) {
   };
   if (article.doi) item.DOI = article.doi;
   if (article.pmid) item.PMID = article.pmid;
+  const custom = {};
+  if (article.arxivId) custom.arxiv_id = article.arxivId;
+  if (article.ericId) custom.eric_id = article.ericId;
+  if (article.scopusId) custom.scopus_id = article.scopusId;
+  if (Object.keys(custom).length > 0) item.custom = custom;
+  if (!article.doi) {
+    if (article.arxivId) {
+      item.URL = `https://arxiv.org/abs/${article.arxivId}`;
+    } else if (article.ericId) {
+      item.URL = `https://eric.ed.gov/?id=${article.ericId}`;
+    }
+  }
   if (article.abstract) item.abstract = article.abstract;
   const dateParts = parseDateParts(article.publicationDate);
   if (dateParts) item.issued = { "date-parts": dateParts };

package/dist/integration/csl-json.js.map

@@ -1 +1 @@
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article.authors[0]!.family.toLowerCase()\n      : 'anon';\n\n  const yearPart = extractYear(article.publicationDate);\n\n  return `${authorPart}-${yearPart}`;\n}\n\n/**\n * Extract year from a publication date string.\n * Handles formats: \"2024-01-15\", \"2024-01\", \"2024\"\n */\nfunction extractYear(date: string | undefined): string {\n  if (!date) return 'nd';\n  const match = date.match(/^(\\d{4})/);\n  return match ? match[1]! : 'nd';\n}\n\n/**\n * Parse a publication date string into CSL date-parts format.\n *\n * - `\"2024-01-15\"` → `[[2024, 1, 15]]`\n * - `\"2024-01\"` → `[[2024, 1]]`\n * - `\"2024\"` → `[[2024]]`\n * - `undefined` or `\"\"` → `undefined`\n */\nexport function parseDateParts(\n  date: string | undefined\n): number[][] | undefined {\n  if (!date) return undefined;\n\n  const parts = date.split('-').map(Number);\n  if (parts.length === 0 || Number.isNaN(parts[0])) return undefined;\n\n  return [parts];\n}\n\n/**\n * Convert a single Article to a CSL-JSON item.\n * The `id` parameter must be pre-generated (with duplicate resolution already applied).\n */\nexport function articleToCslJson(article: Article, id: string): CslJsonItem {\n  const item: CslJsonItem = {\n    id,\n    type: 'article-journal',\n    title: article.title,\n    author: article.authors.map((a) => {\n      const entry: { family: string; given?: string } = { family: a.family };\n      if (a.given) entry.given = a.given;\n      return entry;\n    }),\n  };\n\n  if (article.doi) item.DOI = article.doi;\n  if (article.pmid) item.PMID = article.pmid;\n  if (article.abstract) item.abstract = article.abstract;\n\n  const dateParts = parseDateParts(article.publicationDate);\n  if (dateParts) item.issued = { 'date-parts': dateParts };\n\n  if (article.journal) item['container-title'] = article.journal;\n  if (article.volume) item.volume = article.volume;\n  if (article.issue) item.issue = article.issue;\n  if (article.pages) item.page = article.pages;\n\n  return item;\n}\n\n/**\n * Convert an array of Articles to CSL-JSON items with duplicate ID resolution.\n *\n * Duplicates within the batch are resolved by appending suffixes:\n * `smith-2024`, `smith-2024a`, `smith-2024b`, ...\n */\nexport function articlesToCslJson(articles: Article[]): CslJsonItem[] {\n  const idCounts = new Map<string, number>();\n  const result: CslJsonItem[] = [];\n\n  for (const article of articles) {\n    const baseId = generateCslId(article);\n    const count = idCounts.get(baseId) ?? 0;\n    idCounts.set(baseId, count + 1);\n\n    let resolvedId: string;\n    if (count === 0) {\n      resolvedId = baseId;\n    } else {\n      // a=97 in ASCII, so suffix is 'a', 'b', 'c', ...\n      resolvedId = `${baseId}${String.fromCharCode(96 + count)}`;\n    }\n\n    result.push(articleToCslJson(article, resolvedId));\n  }\n\n  return result;\n}\n"],"names":[],"mappings":"AA+BO,SAAS,cAAc,SAA0B;AACtD,QAAM,aACJ,QAAQ,QAAQ,SAAS,IACrB,QAAQ,QAAQ,CAAC,EAAG,OAAO,YAAA,IAC3B;AAEN,QAAM,WAAW,YAAY,QAAQ,eAAe;AAEpD,SAAO,GAAG,UAAU,IAAI,QAAQ;AAClC;AAMA,SAAS,YAAY,MAAkC;AACrD,MAAI,CAAC,KAAM,QAAO;AAClB,QAAM,QAAQ,KAAK,MAAM,UAAU;AACnC,SAAO,QAAQ,MAAM,CAAC,IAAK;AAC7B;AAUO,SAAS,eACd,MACwB;AACxB,MAAI,CAAC,KAAM,QAAO;AAElB,QAAM,QAAQ,KAAK,MAAM,GAAG,EAAE,IAAI,MAAM;AACxC,MAAI,MAAM,WAAW,KAAK,OAAO,MAAM,MAAM,CAAC,CAAC,EAAG,QAAO;AAEzD,SAAO,CAAC,KAAK;AACf;AAMO,SAAS,iBAAiB,SAAkB,IAAyB;AAC1E,QAAM,OAAoB;AAAA,IACxB;AAAA,IACA,MAAM;AAAA,IACN,OAAO,QAAQ;AAAA,IACf,QAAQ,QAAQ,QAAQ,IAAI,CAAC,MAAM;AACjC,YAAM,QAA4C,EAAE,QAAQ,EAAE,OAAA;AAC9D,UAAI,EAAE,MAAO,OAAM,QAAQ,EAAE;AAC7B,aAAO;AAAA,IACT,CAAC;AAAA,EAAA;AAGH,MAAI,QAAQ,IAAK,MAAK,MAAM,QAAQ;AACpC,MAAI,QAAQ,KAAM,MAAK,OAAO,QAAQ;AACtC,MAAI,QAAQ,SAAU,MAAK,WAAW,QAAQ;AAE9C,QAAM,YAAY,eAAe,QAAQ,eAAe;AACxD,MAAI,UAAW,MAAK,SAAS,EAAE,cAAc,UAAA;AAE7C,MAAI,QAAQ,QAAS,MAAK,iBAAiB,IAAI,QAAQ;AACvD,MAAI,QAAQ,OAAQ,MAAK,SAAS,QAAQ;AAC1C,MAAI,QAAQ,MAAO,MAAK,QAAQ,QAAQ;AACxC,MAAI,QAAQ,MAAO,MAAK,OAAO,QAAQ;AAEvC,SAAO;AACT;AAQO,SAAS,kBAAkB,UAAoC;AACpE,QAAM,+BAAe,IAAA;AACrB,QAAM,SAAwB,CAAA;AAE9B,aAAW,WAAW,UAAU;AAC9B,UAAM,SAAS,cAAc,OAAO;AACpC,UAAM,QAAQ,SAAS,IAAI,MAAM,KAAK;AACtC,aAAS,IAAI,QAAQ,QAAQ,CAAC;AAE9B,QAAI;AACJ,QAAI,UAAU,GAAG;AACf,mBAAa;AAAA,IACf,OAAO;AAEL,mBAAa,GAAG,MAAM,GAAG,OAAO,aAAa,KAAK,KAAK,CAAC;AAAA,IAC1D;AAEA,WAAO,KAAK,iBAAiB,SAAS,UAAU,CAAC;AAAA,EACnD;AAEA,SAAO;AACT;"}
+{"version":3,"file":"csl-json.js","sources":["../../src/integration/csl-json.ts"],"sourcesContent":["/**\n * CSL-JSON conversion module.\n * Converts Article objects to CSL-JSON format for bulk import via ref add -i json.\n */\n\nimport type { Article } from '../providers/base/types.js';\n\n/** CSL-JSON item type used for bulk import. */\nexport interface CslJsonItem {\n  id: string;\n  type: string;\n  title: string;\n  author: Array<{ family: string; given?: string }>;\n  DOI?: string;\n  PMID?: string;\n  URL?: string;\n  abstract?: string;\n  issued?: { 'date-parts': number[][] };\n  'container-title'?: string;\n  volume?: string;\n  issue?: string;\n  page?: string;\n  /**\n   * Alternative identifiers. Key names match what reference-manager reads:\n   * its duplicate detector and fulltext discovery use `custom.arxiv_id`.\n   */\n  custom?: {\n    arxiv_id?: string;\n    eric_id?: string;\n    scopus_id?: string;\n  };\n}\n\n/**\n * Generate a human-readable CSL ID from an article (author-year format).\n *\n * Format: `{first-author-family}-{year}`\n * - No author: `anon-{year}`\n * - No year: `{author}-nd`\n * - Duplicate resolution is handled by `articlesToCslJson()` at the batch level.\n */\nexport function generateCslId(article: Article): string {\n  const authorPart =\n    article.authors.length > 0\n      ? article.authors[0]!.family.toLowerCase()\n      : 'anon';\n\n  const yearPart = extractYear(article.publicationDate);\n\n  return `${authorPart}-${yearPart}`;\n}\n\n/**\n * Extract year from a publication date string.\n * Handles formats: \"2024-01-15\", \"2024-01\", \"2024\"\n */\nfunction extractYear(date: string | undefined): string {\n  if (!date) return 'nd';\n  const match = date.match(/^(\\d{4})/);\n  return match ? match[1]! : 'nd';\n}\n\n/**\n * Parse a publication date string into CSL date-parts format.\n *\n * - `\"2024-01-15\"` → `[[2024, 1, 15]]`\n * - `\"2024-01\"` → `[[2024, 1]]`\n * - `\"2024\"` → `[[2024]]`\n * - `undefined` or `\"\"` → `undefined`\n */\nexport function parseDateParts(\n  date: string | undefined\n): number[][] | undefined {\n  if (!date) return undefined;\n\n  const parts = date.split('-').map(Number);\n  if (parts.length === 0 || Number.isNaN(parts[0])) return undefined;\n\n  return [parts];\n}\n\n/**\n * Convert a single Article to a CSL-JSON item.\n * The `id` parameter must be pre-generated (with duplicate resolution already applied).\n */\nexport function articleToCslJson(article: Article, id: string): CslJsonItem {\n  const item: CslJsonItem = {\n    id,\n    type: 'article-journal',\n    title: article.title,\n    author: article.authors.map((a) => {\n      const entry: { family: string; given?: string } = { family: a.family };\n      if (a.given) entry.given = a.given;\n      return entry;\n    }),\n  };\n\n  if (article.doi) item.DOI = article.doi;\n  if (article.pmid) item.PMID = article.pmid;\n\n  const custom: NonNullable<CslJsonItem['custom']> = {};\n  if (article.arxivId) custom.arxiv_id = article.arxivId;\n  if (article.ericId) custom.eric_id = article.ericId;\n  if (article.scopusId) custom.scopus_id = article.scopusId;\n  if (Object.keys(custom).length > 0) item.custom = custom;\n\n  // Without a DOI, give resolvers a landing page for the alternative identifier\n  if (!article.doi) {\n    if (article.arxivId) {\n      item.URL = `https://arxiv.org/abs/${article.arxivId}`;\n    } else if (article.ericId) {\n      item.URL = `https://eric.ed.gov/?id=${article.ericId}`;\n    }\n  }\n\n  if (article.abstract) item.abstract = article.abstract;\n\n  const dateParts = parseDateParts(article.publicationDate);\n  if (dateParts) item.issued = { 'date-parts': dateParts };\n\n  if (article.journal) item['container-title'] = article.journal;\n  if (article.volume) item.volume = article.volume;\n  if (article.issue) item.issue = article.issue;\n  if (article.pages) item.page = article.pages;\n\n  return item;\n}\n\n/**\n * Convert an array of Articles to CSL-JSON items with duplicate ID resolution.\n *\n * Duplicates within the batch are resolved by appending suffixes:\n * `smith-2024`, `smith-2024a`, `smith-2024b`, ...\n */\nexport function articlesToCslJson(articles: Article[]): CslJsonItem[] {\n  const idCounts = new Map<string, number>();\n  const result: CslJsonItem[] = [];\n\n  for (const article of articles) {\n    const baseId = generateCslId(article);\n    const count = idCounts.get(baseId) ?? 0;\n    idCounts.set(baseId, count + 1);\n\n    let resolvedId: string;\n    if (count === 0) {\n      resolvedId = baseId;\n    } else {\n      // a=97 in ASCII, so suffix is 'a', 'b', 'c', ...\n      resolvedId = `${baseId}${String.fromCharCode(96 + count)}`;\n    }\n\n    result.push(articleToCslJson(article, resolvedId));\n  }\n\n  return result;\n}\n"],"names":[],"mappings":"AAyCO,SAAS,cAAc,SAA0B;AACtD,QAAM,aACJ,QAAQ,QAAQ,SAAS,IACrB,QAAQ,QAAQ,CAAC,EAAG,OAAO,YAAA,IAC3B;AAEN,QAAM,WAAW,YAAY,QAAQ,eAAe;AAEpD,SAAO,GAAG,UAAU,IAAI,QAAQ;AAClC;AAMA,SAAS,YAAY,MAAkC;AACrD,MAAI,CAAC,KAAM,QAAO;AAClB,QAAM,QAAQ,KAAK,MAAM,UAAU;AACnC,SAAO,QAAQ,MAAM,CAAC,IAAK;AAC7B;AAUO,SAAS,eACd,MACwB;AACxB,MAAI,CAAC,KAAM,QAAO;AAElB,QAAM,QAAQ,KAAK,MAAM,GAAG,EAAE,IAAI,MAAM;AACxC,MAAI,MAAM,WAAW,KAAK,OAAO,MAAM,MAAM,CAAC,CAAC,EAAG,QAAO;AAEzD,SAAO,CAAC,KAAK;AACf;AAMO,SAAS,iBAAiB,SAAkB,IAAyB;AAC1E,QAAM,OAAoB;AAAA,IACxB;AAAA,IACA,MAAM;AAAA,IACN,OAAO,QAAQ;AAAA,IACf,QAAQ,QAAQ,QAAQ,IAAI,CAAC,MAAM;AACjC,YAAM,QAA4C,EAAE,QAAQ,EAAE,OAAA;AAC9D,UAAI,EAAE,MAAO,OAAM,QAAQ,EAAE;AAC7B,aAAO;AAAA,IACT,CAAC;AAAA,EAAA;AAGH,MAAI,QAAQ,IAAK,MAAK,MAAM,QAAQ;AACpC,MAAI,QAAQ,KAAM,MAAK,OAAO,QAAQ;AAEtC,QAAM,SAA6C,CAAA;AACnD,MAAI,QAAQ,QAAS,QAAO,WAAW,QAAQ;AAC/C,MAAI,QAAQ,OAAQ,QAAO,UAAU,QAAQ;AAC7C,MAAI,QAAQ,SAAU,QAAO,YAAY,QAAQ;AACjD,MAAI,OAAO,KAAK,MAAM,EAAE,SAAS,QAAQ,SAAS;AAGlD,MAAI,CAAC,QAAQ,KAAK;AAChB,QAAI,QAAQ,SAAS;AACnB,WAAK,MAAM,yBAAyB,QAAQ,OAAO;AAAA,IACrD,WAAW,QAAQ,QAAQ;AACzB,WAAK,MAAM,2BAA2B,QAAQ,MAAM;AAAA,IACtD;AAAA,EACF;AAEA,MAAI,QAAQ,SAAU,MAAK,WAAW,QAAQ;AAE9C,QAAM,YAAY,eAAe,QAAQ,eAAe;AACxD,MAAI,UAAW,MAAK,SAAS,EAAE,cAAc,UAAA;AAE7C,MAAI,QAAQ,QAAS,MAAK,iBAAiB,IAAI,QAAQ;AACvD,MAAI,QAAQ,OAAQ,MAAK,SAAS,QAAQ;AAC1C,MAAI,QAAQ,MAAO,MAAK,QAAQ,QAAQ;AACxC,MAAI,QAAQ,MAAO,MAAK,OAAO,QAAQ;AAEvC,SAAO;AACT;AAQO,SAAS,kBAAkB,UAAoC;AACpE,QAAM,+BAAe,IAAA;AACrB,QAAM,SAAwB,CAAA;AAE9B,aAAW,WAAW,UAAU;AAC9B,UAAM,SAAS,cAAc,OAAO;AACpC,UAAM,QAAQ,SAAS,IAAI,MAAM,KAAK;AACtC,aAAS,IAAI,QAAQ,QAAQ,CAAC;AAE9B,QAAI;AACJ,QAAI,UAAU,GAAG;AACf,mBAAa;AAAA,IACf,OAAO;AAEL,mBAAa,GAAG,MAAM,GAAG,OAAO,aAAa,KAAK,KAAK,CAAC;AAAA,IAC1D;AAEA,WAAO,KAAK,iBAAiB,SAAS,UAAU,CAAC;AAAA,EACnD;AAEA,SAAO;AACT;"}

package/dist/integration/register.d.ts.map

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package/dist/integration/register.js

@@ -12,7 +12,7 @@ async function saveRegistrationRecord(sessionDir, record) {
   await fs.writeFile(filePath, JSON.stringify(record, null, 2));
 }
 function hasIdentifier(article) {
-  return !!(article.pmid || article.doi);
+  return !!(article.pmid || article.doi || article.arxivId || article.scopusId || article.ericId);
 }
 async function registerArticles(articles, options) {
   const { sessionId, sessionDir, withAbstracts, noAttachFulltext, onProgress, onAttachProgress } = options;

package/dist/integration/register.js.map

@@ -1 +1 @@
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+{"version":3,"file":"register.js","sources":["../../src/integration/register.ts"],"sourcesContent":["/**\n * Registration logic for reference-manager integration.\n * Uses bulk CSL-JSON import for performance.\n */\n\nimport * as fs from 'node:fs/promises';\nimport * as path from 'node:path';\nimport type { Article } from '../providers/base/types.js';\nimport { RegistrationRecordSchema, type RegistrationRecord } from './types.js';\nimport { refAddBulk } from './ref-cli.js';\nimport { articlesToCslJson } from './csl-json.js';\nimport { attachFulltexts } from './fulltext-attach.js';\n\nconst REGISTRATION_FILE = 'registration.json';\nconst BULK_IMPORT_FILE = '_bulk_import.json';\n\n/**\n * Save registration record to session directory.\n */\nexport async function saveRegistrationRecord(\n  sessionDir: string,\n  record: RegistrationRecord\n): Promise<void> {\n  await fs.mkdir(sessionDir, { recursive: true });\n  const filePath = path.join(sessionDir, REGISTRATION_FILE);\n  await fs.writeFile(filePath, JSON.stringify(record, null, 2));\n}\n\n/**\n * Load registration record from session directory.\n * Returns null if file does not exist.\n * Throws if file exists but is invalid.\n */\nexport async function loadRegistrationRecord(\n  sessionDir: string\n): Promise<RegistrationRecord | null> {\n  const filePath = path.join(sessionDir, REGISTRATION_FILE);\n  try {\n    const content = await fs.readFile(filePath, 'utf-8');\n    const data = JSON.parse(content);\n    return RegistrationRecordSchema.parse(data);\n  } catch (error) {\n    // File not found - return null\n    if (error instanceof Error && 'code' in error && error.code === 'ENOENT') {\n      return null;\n    }\n    // Parse or validation error - re-throw\n    throw error;\n  }\n}\n\n/**\n * Options for registerArticles function.\n */\nexport interface RegisterOptions {\n  sessionId: string;\n  sessionDir: string;\n  withAbstracts?: boolean;\n  /** Skip fulltext attach step */\n  noAttachFulltext?: boolean;\n  onProgress?: (current: number, total: number) => void;\n  onAttachProgress?: (current: number, total: number) => void;\n}\n\n/**\n * Check if an article has an identifier suitable for registration.\n * Any of DOI / PMID / arXiv ID / Scopus ID / ERIC ID qualifies;\n * only articles with none of these are counted as noId and skipped.\n */\nfunction hasIdentifier(article: Article): boolean {\n  return !!(\n    article.pmid ||\n    article.doi ||\n    article.arxivId ||\n    article.scopusId ||\n    article.ericId\n  );\n}\n\n/**\n * Register articles with reference-manager using bulk CSL-JSON import.\n *\n * Flow:\n * 1. 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package/dist/node_modules/@ncukondo/academic-fulltext/dist/convert/jats-parser.js

@@ -724,6 +724,29 @@ function parseSection(secChildren, level) {
   }
   return { title, level, content, subsections };
 }
+function flushBlockBuffer(buffer, sections) {
+  const content = parseBlockContent(buffer);
+  if (content.length > 0) {
+    sections.push({ title: "", level: 2, content, subsections: [] });
+  }
+}
+function parseMixedBodyChildren(children, sections) {
+  let blockBuffer = [];
+  for (const child of children) {
+    if (getTagName(child) === "sec") {
+      if (blockBuffer.length > 0) {
+        flushBlockBuffer(blockBuffer, sections);
+        blockBuffer = [];
+      }
+      sections.push(parseSection(getChildren(child), 2));
+    } else {
+      blockBuffer.push(child);
+    }
+  }
+  if (blockBuffer.length > 0) {
+    flushBlockBuffer(blockBuffer, sections);
+  }
+}
 function parseJatsBody(xml) {
   const parsed = parser.parse(xml);
   const article = findArticle(parsed);
@@ -735,14 +758,9 @@ function parseJatsBody(xml) {
   const sections = [];
   const secs = findChildren(body.children, "sec");
   if (secs.length > 0) {
-    for (const sec of secs) {
-      sections.push(parseSection(sec.children, 2));
-    }
+    parseMixedBodyChildren(body.children, sections);
   } else {
-    const content = parseBlockContent(body.children);
-    if (content.length > 0) {
-      sections.push({ title: "", level: 2, content, subsections: [] });
-    }
+    flushBlockBuffer(body.children, sections);
   }
   return sections;
 }