@ncukondo/search-hub 0.13.0 → 0.15.0

package/README.md

@@ -8,9 +8,14 @@ A CLI tool for systematic literature searching across multiple academic database
 ## Features
 
 - **Multi-database search**: PubMed, ERIC, arXiv, Scopus (Web of Science, Embase planned)
-- **Unified query syntax**: YAML-based DSL with automatic translation
+- **Unified query syntax**: YAML-based DSL with automatic translation and JSON Schema support
+- **Controlled vocabulary validation**: Validates MeSH, ERIC descriptors, and Emtree terms with typo suggestions
 - **Reproducible searches**: Full session logging for PRISMA reporting
+- **Result filtering**: Flexible query expressions (`-q`) to search and filter results by title, abstract, author, year, and more
+- **Coverage verification**: Check whether known articles appear in search results for query quality validation
+- **Session comparison**: Diff results between query iterations to track refinements
 - **Resume support**: Continue interrupted searches at DB or page level
+- **Review workflow**: Multi-reviewer screening with agreement tracking and finalization
 - **Fulltext management**: OA discovery, automatic retrieval, PMC XML to Markdown conversion
 - **Reference manager integration**: Works with [reference-manager](https://github.com/ncukondo/reference-manager)
 
@@ -37,8 +42,15 @@ This creates config and data directories in platform-specific locations:
 | macOS | `~/Library/Preferences/search-hub/` | `~/Library/Application Support/search-hub/` |
 | Windows | `%APPDATA%/search-hub/Config/` | `%LOCALAPPDATA%/search-hub/Data/` |
 
-2. Create a query file (`query.yaml`):
+2. Create a query file:
+```bash
+search-hub query init -o query.yaml
+```
+
+This generates a YAML template with JSON Schema support for editor autocompletion. Edit it to define your search:
+
 ```yaml
+# yaml-language-server: $schema=./query.schema.json
 name: my_review
 description: "Literature search for scoping review"
 
@@ -56,12 +68,19 @@ filters:
     - en
 ```
 
-3. Run search:
+3. Validate the query:
+```bash
+search-hub query validate query.yaml
+```
+
+This checks structure, validates controlled vocabulary terms (MeSH, ERIC descriptors, Emtree) against external APIs, and suggests corrections for typos.
+
+4. Run search:
 ```bash
 search-hub search query.yaml
 ```
 
-4. Export results:
+5. Export results:
 ```bash
 search-hub export <session-id> --format ids
 ```
@@ -80,20 +99,26 @@ Developing an effective search query is iterative. Start broad, then refine base
 2. **Review initial results** - Check titles to assess quality:
    ```bash
    search-hub results <session-v1> --limit 50
+   search-hub results <session-v1> -q "title:diabetes year:2023-2025"
+   ```
+
+3. **Check coverage** - Verify known relevant articles are captured:
+   ```bash
+   search-hub check <session-v1> --file known-articles.txt
    ```
 
-3. **Refine the query** - Copy and modify your query file:
+4. **Refine the query** - Copy and modify your query file:
    ```bash
    cp query-v1.yaml query-v2.yaml
    # Edit query-v2.yaml to add/remove terms, adjust filters
    ```
 
-4. **Run the refined search**:
+5. **Run the refined search**:
    ```bash
    search-hub search query-v2.yaml --max-results 100
    ```
 
-5. **Compare results with diff** - See what changed:
+6. **Compare results with diff** - See what changed:
    ```bash
    search-hub diff <session-v1> <session-v2> --show removed
    ```
@@ -106,6 +131,11 @@ Developing an effective search query is iterative. Start broad, then refine base
   search-hub search query.yaml --count-only
   ```
 
+- **Use `--preview`** to see hit counts with sample titles:
+  ```bash
+  search-hub search query.yaml --preview
+  ```
+
 - **Use `--dry-run`** to preview translations: See exactly what query each database will receive.
   ```bash
   search-hub search query.yaml --dry-run
@@ -139,10 +169,10 @@ See [Fulltext Management Guide](./docs/fulltext.md) for details.
 
 ## Documentation
 
-- [Query Guide](./docs/query-guide.md) - How to write query files
+- [Query Guide](./docs/query-guide.md) - How to write query files (DSL, JSON Schema, vocabulary validation)
 - [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
+- [Databases](./docs/databases.md) - Supported databases, controlled vocabularies, and tips
 - [Fulltext Management](./docs/fulltext.md) - Fulltext retrieval and management
 
 ## Development

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

@@ -0,0 +1,34 @@
+import { Article, ProviderName } from '../../providers/base/types.js';
+export interface ParsedIdentifier {
+    type: 'doi' | 'pmid' | 'arxiv';
+    value: string;
+    raw: string;
+}
+export declare function parseIdentifierFile(content: string): ParsedIdentifier[];
+export interface FoundItem {
+    query: string;
+    type: ParsedIdentifier['type'];
+    sources: ProviderName[];
+    title: string;
+}
+export interface MissingItem {
+    query: string;
+    type: ParsedIdentifier['type'];
+}
+export interface CheckResult {
+    total: number;
+    foundCount: number;
+    missingCount: number;
+    coverage: number;
+    found: FoundItem[];
+    missing: MissingItem[];
+}
+export declare function checkCoverage(articles: Article[], identifiers: ParsedIdentifier[]): CheckResult;
+export interface FormatCheckOptions {
+    sessionId: string;
+    source: string;
+    missingOnly?: boolean | undefined;
+}
+export declare function formatCheckResult(result: CheckResult, options: FormatCheckOptions): string;
+export declare function formatCheckResultJson(result: CheckResult, options: FormatCheckOptions): string;
+//# sourceMappingURL=check.d.ts.map

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

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

@@ -0,0 +1,126 @@
+import { getArticleKeys } from "./session-utils.js";
+function parseIdentifierFile(content) {
+  const results = [];
+  const lines = content.split("\n");
+  for (let i = 0; i < lines.length; i++) {
+    const trimmed = lines[i].trim();
+    if (trimmed === "" || trimmed.startsWith("#")) continue;
+    const parsed = parseLine(trimmed, i + 1);
+    results.push(parsed);
+  }
+  return results;
+}
+function parseLine(line, lineNumber) {
+  const prefixMatch = line.match(/^(doi|pmid|arxiv):(.+)$/i);
+  if (prefixMatch) {
+    const prefix = prefixMatch[1].toLowerCase();
+    return { type: prefix, value: prefixMatch[2].trim(), raw: line };
+  }
+  if (line.startsWith("10.")) {
+    return { type: "doi", value: line, raw: line };
+  }
+  if (/^\d+$/.test(line)) {
+    return { type: "pmid", value: line, raw: line };
+  }
+  throw new Error(`Unrecognizable identifier at line ${lineNumber}: ${line}`);
+}
+function checkCoverage(articles, identifiers) {
+  if (identifiers.length === 0) {
+    return { total: 0, foundCount: 0, missingCount: 0, coverage: 0, found: [], missing: [] };
+  }
+  const keyToArticles = /* @__PURE__ */ new Map();
+  for (const article of articles) {
+    for (const key of getArticleKeys(article)) {
+      const existing = keyToArticles.get(key);
+      if (existing) {
+        existing.push(article);
+      } else {
+        keyToArticles.set(key, [article]);
+      }
+    }
+  }
+  const found = [];
+  const missing = [];
+  for (const id of identifiers) {
+    const key = identifierToKey(id);
+    const matched = keyToArticles.get(key);
+    if (matched && matched.length > 0) {
+      const sources = [...new Set(matched.map((a) => a.source))];
+      found.push({
+        query: id.raw,
+        type: id.type,
+        sources,
+        title: matched[0].title
+      });
+    } else {
+      missing.push({ query: id.raw, type: id.type });
+    }
+  }
+  const total = identifiers.length;
+  return {
+    total,
+    foundCount: found.length,
+    missingCount: missing.length,
+    coverage: found.length / total,
+    found,
+    missing
+  };
+}
+function identifierToKey(id) {
+  if (id.type === "doi") {
+    return `doi:${id.value.toLowerCase()}`;
+  }
+  return `${id.type}:${id.value}`;
+}
+function formatCheckResult(result, options) {
+  const lines = [];
+  const pct = result.total > 0 ? (result.coverage * 100).toFixed(1) : "0.0";
+  lines.push(`Coverage: ${options.sessionId}`);
+  lines.push(`Source: ${options.source} (${result.total} identifiers)`);
+  lines.push("");
+  lines.push(`Found: ${result.foundCount}/${result.total} (${pct}%)`);
+  if (result.missing.length > 0) {
+    lines.push("");
+    lines.push(`Missing (${result.missingCount}):`);
+    for (const m of result.missing) {
+      lines.push(`  ${m.query}`);
+    }
+  }
+  if (!options.missingOnly && result.found.length > 0) {
+    lines.push("");
+    lines.push(`Found (${result.foundCount}):`);
+    for (const f of result.found) {
+      lines.push(`  ${f.query} → ${f.title} (${f.sources.join(", ")})`);
+    }
+  }
+  return lines.join("\n");
+}
+function formatCheckResultJson(result, options) {
+  return JSON.stringify({
+    session: options.sessionId,
+    source: options.source,
+    total: result.total,
+    found: result.foundCount,
+    missing: result.missingCount,
+    coverage: result.coverage,
+    details: {
+      found: result.found.map((f) => ({
+        query: f.query,
+        type: f.type,
+        sources: f.sources,
+        title: f.title
+      })),
+      missing: result.missing.map((m) => ({
+        query: m.query,
+        type: m.type
+      }))
+    }
+  }, null, 2);
+}
+export {
+  checkCoverage,
+  formatCheckResult,
+  formatCheckResultJson,
+  parseIdentifierFile
+};
+//# sourceMappingURL=check.js.map

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

@@ -0,0 +1 @@
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(result.coverage * 100).toFixed(1) : '0.0';\n\n  lines.push(`Coverage: ${options.sessionId}`);\n  lines.push(`Source: ${options.source} (${result.total} identifiers)`);\n  lines.push('');\n  lines.push(`Found: ${result.foundCount}/${result.total} (${pct}%)`);\n\n  if (result.missing.length > 0) {\n    lines.push('');\n    lines.push(`Missing (${result.missingCount}):`);\n    for (const m of result.missing) {\n      lines.push(`  ${m.query}`);\n    }\n  }\n\n  if (!options.missingOnly && result.found.length > 0) {\n    lines.push('');\n    lines.push(`Found (${result.foundCount}):`);\n    for (const f of result.found) {\n      lines.push(`  ${f.query} → ${f.title} (${f.sources.join(', ')})`);\n    }\n  }\n\n  return lines.join('\\n');\n}\n\nexport function formatCheckResultJson(result: CheckResult, options: FormatCheckOptions): string {\n  return JSON.stringify({\n    session: options.sessionId,\n    source: options.source,\n    total: result.total,\n    found: result.foundCount,\n    missing: result.missingCount,\n    coverage: result.coverage,\n    details: {\n      found: result.found.map(f => ({\n        query: f.query,\n        type: f.type,\n        sources: f.sources,\n        title: f.title,\n      })),\n      missing: result.missing.map(m => ({\n        query: m.query,\n        type: m.type,\n      })),\n    },\n  }, null, 2);\n}\n"],"names":[],"mappings":";AAaO,SAAS,oBAAoB,SAAqC;AACvE,QAAM,UAA8B,CAAA;AACpC,QAAM,QAAQ,QAAQ,MAAM,IAAI;AAEhC,WAAS,IAAI,GAAG,IAAI,MAAM,QAAQ,KAAK;AACrC,UAAM,UAAU,MAAM,CAAC,EAAG,KAAA;AAC1B,QAAI,YAAY,MAAM,QAAQ,WAAW,GAAG,EAAG;AAE/C,UAAM,SAAS,UAAU,SAAS,IAAI,CAAC;AACvC,YAAQ,KAAK,MAAM;AAAA,EACrB;AAEA,SAAO;AACT;AAEA,SAAS,UAAU,MAAc,YAAsC;AAErE,QAAM,cAAc,KAAK,MAAM,0BAA0B;AACzD,MAAI,aAAa;AACf,UAAM,SAAS,YAAY,CAAC,EAAG,YAAA;AAC/B,WAAO,EAAE,MAAM,QAAQ,OAAO,YAAY,CAAC,EAAG,KAAA,GAAQ,KAAK,KAAA;AAAA,EAC7D;AAGA,MAAI,KAAK,WAAW,KAAK,GAAG;AAC1B,WAAO,EAAE,MAAM,OAAO,OAAO,MAAM,KAAK,KAAA;AAAA,EAC1C;AAGA,MAAI,QAAQ,KAAK,IAAI,GAAG;AACtB,WAAO,EAAE,MAAM,QAAQ,OAAO,MAAM,KAAK,KAAA;AAAA,EAC3C;AAEA,QAAM,IAAI,MAAM,qCAAqC,UAAU,KAAK,IAAI,EAAE;AAC5E;AAuBO,SAAS,cAAc,UAAqB,aAA8C;AAC/F,MAAI,YAAY,WAAW,GAAG;AAC5B,WAAO,EAAE,OAAO,GAAG,YAAY,GAAG,cAAc,GAAG,UAAU,GAAG,OAAO,CAAA,GAAI,SAAS,CAAA,EAAC;AAAA,EACvF;AAGA,QAAM,oCAAoB,IAAA;AAC1B,aAAW,WAAW,UAAU;AAC9B,eAAW,OAAO,eAAe,OAAO,GAAG;AACzC,YAAM,WAAW,cAAc,IAAI,GAAG;AACtC,UAAI,UAAU;AACZ,iBAAS,KAAK,OAAO;AAAA,MACvB,OAAO;AACL,sBAAc,IAAI,KAAK,CAAC,OAAO,CAAC;AAAA,MAClC;AAAA,IACF;AAAA,EACF;AAEA,QAAM,QAAqB,CAAA;AAC3B,QAAM,UAAyB,CAAA;AAE/B,aAAW,MAAM,aAAa;AAC5B,UAAM,MAAM,gBAAgB,EAAE;AAC9B,UAAM,UAAU,cAAc,IAAI,GAAG;AAErC,QAAI,WAAW,QAAQ,SAAS,GAAG;AACjC,YAAM,UAAU,CAAC,GAAG,IAAI,IAAI,QAAQ,IAAI,CAAA,MAAK,EAAE,MAAM,CAAC,CAAC;AACvD,YAAM,KAAK;AAAA,QACT,OAAO,GAAG;AAAA,QACV,MAAM,GAAG;AAAA,QACT;AAAA,QACA,OAAO,QAAQ,CAAC,EAAG;AAAA,MAAA,CACpB;AAAA,IACH,OAAO;AACL,cAAQ,KAAK,EAAE,OAAO,GAAG,KAAK,MAAM,GAAG,MAAM;AAAA,IAC/C;AAAA,EACF;AAEA,QAAM,QAAQ,YAAY;AAC1B,SAAO;AAAA,IACL;AAAA,IACA,YAAY,MAAM;AAAA,IAClB,cAAc,QAAQ;AAAA,IACtB,UAAU,MAAM,SAAS;AAAA,IACzB;AAAA,IACA;AAAA,EAAA;AAEJ;AAEA,SAAS,gBAAgB,IAA8B;AACrD,MAAI,GAAG,SAAS,OAAO;AACrB,WAAO,OAAO,GAAG,MAAM,YAAA,CAAa;AAAA,EACtC;AACA,SAAO,GAAG,GAAG,IAAI,IAAI,GAAG,KAAK;AAC/B;AAQO,SAAS,kBAAkB,QAAqB,SAAqC;AAC1F,QAAM,QAAkB,CAAA;AACxB,QAAM,MAAM,OAAO,QAAQ,KAAK,OAAO,WAAW,KAAK,QAAQ,CAAC,IAAI;AAEpE,QAAM,KAAK,aAAa,QAAQ,SAAS,EAAE;AAC3C,QAAM,KAAK,WAAW,QAAQ,MAAM,KAAK,OAAO,KAAK,eAAe;AACpE,QAAM,KAAK,EAAE;AACb,QAAM,KAAK,UAAU,OAAO,UAAU,IAAI,OAAO,KAAK,KAAK,GAAG,IAAI;AAElE,MAAI,OAAO,QAAQ,SAAS,GAAG;AAC7B,UAAM,KAAK,EAAE;AACb,UAAM,KAAK,YAAY,OAAO,YAAY,IAAI;AAC9C,eAAW,KAAK,OAAO,SAAS;AAC9B,YAAM,KAAK,KAAK,EAAE,KAAK,EAAE;AAAA,IAC3B;AAAA,EACF;AAEA,MAAI,CAAC,QAAQ,eAAe,OAAO,MAAM,SAAS,GAAG;AACnD,UAAM,KAAK,EAAE;AACb,UAAM,KAAK,UAAU,OAAO,UAAU,IAAI;AAC1C,eAAW,KAAK,OAAO,OAAO;AAC5B,YAAM,KAAK,KAAK,EAAE,KAAK,MAAM,EAAE,KAAK,KAAK,EAAE,QAAQ,KAAK,IAAI,CAAC,GAAG;AAAA,IAClE;AAAA,EACF;AAEA,SAAO,MAAM,KAAK,IAAI;AACxB;AAEO,SAAS,sBAAsB,QAAqB,SAAqC;AAC9F,SAAO,KAAK,UAAU;AAAA,IACpB,SAAS,QAAQ;AAAA,IACjB,QAAQ,QAAQ;AAAA,IAChB,OAAO,OAAO;AAAA,IACd,OAAO,OAAO;AAAA,IACd,SAAS,OAAO;AAAA,IAChB,UAAU,OAAO;AAAA,IACjB,SAAS;AAAA,MACP,OAAO,OAAO,MAAM,IAAI,CAAA,OAAM;AAAA,QAC5B,OAAO,EAAE;AAAA,QACT,MAAM,EAAE;AAAA,QACR,SAAS,EAAE;AAAA,QACX,OAAO,EAAE;AAAA,MAAA,EACT;AAAA,MACF,SAAS,OAAO,QAAQ,IAAI,CAAA,OAAM;AAAA,QAChC,OAAO,EAAE;AAAA,QACT,MAAM,EAAE;AAAA,MAAA,EACR;AAAA,IAAA;AAAA,EACJ,GACC,MAAM,CAAC;AACZ;"}

package/dist/cli/commands/export.d.ts

@@ -1,4 +1,4 @@
-import { ProviderName, Article } from '../../providers/base/types.js';
+import { Article } from '../../providers/base/types.js';
 export type ExportFormat = 'ids' | 'json' | 'jsonl' | 'csl-json';
 export type IdType = 'doi' | 'pmid' | 'all';
 export interface ExportFilter {
@@ -11,14 +11,16 @@ export interface ExportCommandOptions {
     sessionId: string;
     format: ExportFormat;
     outputPath?: string;
-    providers?: ProviderName[];
     idType?: IdType;
 }
 export interface CommandLineOptions {
     format?: string | undefined;
     output?: string | undefined;
-    db?: string | undefined;
     idType?: string | undefined;
+    query?: string | undefined;
+    filterYear?: string | undefined;
+    filterTitle?: string | undefined;
+    filterAbstract?: string | undefined;
 }
 export interface ValidationResult {
     valid: boolean;

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

@@ -1 +1 @@
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package/dist/cli/commands/export.js

@@ -1,4 +1,3 @@
-import { parseProviderNames } from "../utils/validation.js";
 import { articlesToCslJson } from "../../integration/csl-json.js";
 import { getArticleKeys } from "./session-utils.js";
 const VALID_FORMATS = ["ids", "json", "jsonl", "csl-json"];
@@ -11,9 +10,6 @@ function parseExportOptions(sessionId, options) {
   if (options.output) {
     result.outputPath = options.output;
   }
-  if (options.db) {
-    result.providers = parseProviderNames(options.db);
-  }
   if (options.idType) {
     result.idType = options.idType;
   }

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

@@ -1 +1 @@
-{"version":3,"file":"export.js","sources":["../../../src/cli/commands/export.ts"],"sourcesContent":["import type { ProviderName } from '../../providers/base/types.js';\nimport type { Article } from '../../providers/base/types.js';\nimport { parseProviderNames } from '../utils/validation.js';\nimport { articlesToCslJson } from '../../integration/csl-json.js';\nimport { getArticleKeys } from './session-utils.js';\n\nexport type ExportFormat = 'ids' | 'json' | 'jsonl' | 'csl-json';\nexport type IdType = 'doi' | 'pmid' | 'all';\n\nexport interface ExportFilter {\n  yearFrom?: number;\n  yearTo?: number;\n  titleKeywords?: string[];\n  abstractKeywords?: string[];\n}\n\nexport interface ExportCommandOptions {\n  sessionId: string;\n  format: ExportFormat;\n  outputPath?: string;\n  providers?: ProviderName[];\n  idType?: IdType;\n}\n\nexport interface CommandLineOptions {\n  format?: string | undefined;\n  output?: string | undefined;\n  db?: string | undefined;\n  idType?: string | undefined;\n}\n\nexport interface ValidationResult {\n  valid: boolean;\n  error?: string;\n}\n\nconst VALID_FORMATS: ExportFormat[] = ['ids', 'json', 'jsonl', 'csl-json'];\nconst VALID_ID_TYPES: IdType[] = ['doi', 'pmid', 'all'];\n\nexport function parseExportOptions(\n  sessionId: string,\n  options: CommandLineOptions\n): ExportCommandOptions {\n  const result: ExportCommandOptions = {\n    sessionId,\n    format: (options.format as ExportFormat) || 'jsonl',\n  };\n\n  if (options.output) {\n    result.outputPath = options.output;\n  }\n\n  if (options.db) {\n    result.providers = parseProviderNames(options.db);\n  }\n\n  if (options.idType) {\n    result.idType = options.idType as IdType;\n  }\n\n  return result;\n}\n\nexport function validateExportInput(options: ExportCommandOptions): ValidationResult {\n  if (!options.sessionId || options.sessionId.trim() === '') {\n    return {\n      valid: false,\n      error: 'A session ID is required',\n    };\n  }\n\n  if (!VALID_FORMATS.includes(options.format)) {\n    return {\n      valid: false,\n      error: `Invalid format: ${options.format}. Valid formats are: ${VALID_FORMATS.join(', ')}`,\n    };\n  }\n\n  if (options.idType) {\n    if (!VALID_ID_TYPES.includes(options.idType)) {\n      return {\n        valid: false,\n        error: `Invalid id-type: ${options.idType}. Valid types are: ${VALID_ID_TYPES.join(', ')}`,\n      };\n    }\n\n    if (options.format !== 'ids') {\n      return {\n        valid: false,\n        error: '--id-type can only be used with --format ids',\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\nexport function formatIds(articles: Article[], idType: IdType): string {\n  if (idType === 'all') {\n    const groups: string[] = [];\n    for (const article of articles) {\n      const ids: string[] = [];\n      if (article.pmid) ids.push(`pmid:${article.pmid}`);\n      if (article.doi) ids.push(`doi:${article.doi}`);\n      if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n      if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n      if (article.ericId) ids.push(`eric:${article.ericId}`);\n      if (ids.length > 0) {\n        groups.push(ids.join('\\n'));\n      }\n    }\n    return groups.join('\\n\\n');\n  }\n\n  const ids: string[] = [];\n  for (const article of articles) {\n    if (idType === 'doi') {\n      if (article.doi) {\n        ids.push(article.doi);\n      }\n    } else if (idType === 'pmid') {\n      if (article.pmid) {\n        ids.push(article.pmid);\n      }\n    }\n  }\n\n  return ids.join('\\n');\n}\n\nfunction extractYear(publicationDate: string | undefined): number | null {\n  if (!publicationDate) return null;\n  const year = parseInt(publicationDate.substring(0, 4), 10);\n  return Number.isNaN(year) ? null : year;\n}\n\nfunction addYearField(articles: Article[]): (Article & { year: number | null })[] {\n  return articles.map((article) => ({\n    ...article,\n    year: extractYear(article.publicationDate),\n  }));\n}\n\nexport interface JsonExportMetadata {\n  sessionId: string;\n  sessionName: string;\n  createdAt: string;\n  databases: Record<string, number>;\n}\n\nexport function formatJson(articles: Article[], metadata?: JsonExportMetadata): string {\n  const articlesWithYear = addYearField(articles);\n\n  if (!metadata) {\n    return JSON.stringify(articlesWithYear, null, 2);\n  }\n\n  return JSON.stringify(\n    {\n      session: {\n        id: metadata.sessionId,\n        name: metadata.sessionName,\n        createdAt: metadata.createdAt,\n      },\n      summary: {\n        totalResults: articles.length,\n        databases: metadata.databases,\n      },\n      results: articlesWithYear,\n    },\n    null,\n    2\n  );\n}\n\nexport function formatJsonl(articles: Article[]): string {\n  if (articles.length === 0) {\n    return '';\n  }\n  return addYearField(articles).map((article) => JSON.stringify(article)).join('\\n');\n}\n\nexport function formatCslJson(articles: Article[]): string {\n  const cslItems = articlesToCslJson(articles);\n  return JSON.stringify(cslItems, null, 2);\n}\n\n\nconst METADATA_FIELDS: (keyof Article)[] = [\n  'doi', 'pmid', 'arxivId', 'scopusId', 'ericId',\n  'abstract', 'publicationDate', 'journal', 'volume', 'issue', 'pages',\n];\n\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  for (const field of METADATA_FIELDS) {\n    if (article[field] !== undefined && article[field] !== '') {\n      count++;\n    }\n  }\n  return count;\n}\n\nexport interface DeduplicationResult {\n  articles: Article[];\n  duplicatesRemoved: number;\n}\n\nexport function deduplicateArticles(articles: Article[]): DeduplicationResult {\n  // Map from identifier key to index in the unique array\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let duplicatesRemoved = 0;\n\n  for (const article of articles) {\n    const keys = getArticleKeys(article);\n\n    if (keys.length === 0) {\n      // No identifiers - cannot deduplicate, keep the article\n      unique.push(article);\n      continue;\n    }\n\n    // Check if any identifier has been seen before\n    let existingIndex: number | undefined;\n    for (const key of keys) {\n      const idx = keyToIndex.get(key);\n      if (idx !== undefined) {\n        existingIndex = idx;\n        break;\n      }\n    }\n\n    if (existingIndex !== undefined) {\n      // Duplicate found - compare metadata richness\n      const existing = unique[existingIndex]!;\n      if (countMetadataFields(article) > countMetadataFields(existing)) {\n        // Replace with the richer record\n        unique[existingIndex] = article;\n        // Update all keys to point to the same index\n        const newKeys = getArticleKeys(article);\n        for (const key of newKeys) {\n          keyToIndex.set(key, existingIndex);\n        }\n      }\n      duplicatesRemoved++;\n    } else {\n      const index = unique.length;\n      unique.push(article);\n      // Map all identifiers to this index\n      for (const key of keys) {\n        keyToIndex.set(key, index);\n      }\n    }\n  }\n\n  return { articles: unique, duplicatesRemoved };\n}\n\nexport function filterArticles(articles: Article[], filter: ExportFilter): Article[] {\n  const hasYearFilter = filter.yearFrom !== undefined || filter.yearTo !== 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Abstract keyword filter (OR within keywords, AND with other filters)\n    if (hasAbstractFilter) {\n      if (!article.abstract) return false;\n      const abstractLower = article.abstract.toLowerCase();\n      const matched = filter.abstractKeywords!.some((kw) => abstractLower.includes(kw.toLowerCase()));\n      if (!matched) return false;\n    }\n\n    return true;\n  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Valid formats are: ${VALID_FORMATS.join(', ')}`,\n    };\n  }\n\n  if (options.idType) {\n    if (!VALID_ID_TYPES.includes(options.idType)) {\n      return {\n        valid: false,\n        error: `Invalid id-type: ${options.idType}. Valid types are: ${VALID_ID_TYPES.join(', ')}`,\n      };\n    }\n\n    if (options.format !== 'ids') {\n      return {\n        valid: false,\n        error: '--id-type can only be used with --format ids',\n      };\n    }\n  }\n\n  return { valid: true };\n}\n\nexport function formatIds(articles: Article[], idType: IdType): string {\n  if (idType === 'all') {\n    const groups: string[] = [];\n    for (const article of articles) {\n      const ids: string[] = [];\n      if (article.pmid) ids.push(`pmid:${article.pmid}`);\n      if (article.doi) ids.push(`doi:${article.doi}`);\n      if (article.arxivId) ids.push(`arxiv:${article.arxivId}`);\n      if (article.scopusId) ids.push(`scopus:${article.scopusId}`);\n      if (article.ericId) ids.push(`eric:${article.ericId}`);\n      if (ids.length > 0) {\n        groups.push(ids.join('\\n'));\n      }\n    }\n    return groups.join('\\n\\n');\n  }\n\n  const ids: string[] = [];\n  for (const article of articles) {\n    if (idType === 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JSON.stringify(articlesWithYear, null, 2);\n  }\n\n  return JSON.stringify(\n    {\n      session: {\n        id: metadata.sessionId,\n        name: metadata.sessionName,\n        createdAt: metadata.createdAt,\n      },\n      summary: {\n        totalResults: articles.length,\n        databases: metadata.databases,\n      },\n      results: articlesWithYear,\n    },\n    null,\n    2\n  );\n}\n\nexport function formatJsonl(articles: Article[]): string {\n  if (articles.length === 0) {\n    return '';\n  }\n  return addYearField(articles).map((article) => JSON.stringify(article)).join('\\n');\n}\n\nexport function formatCslJson(articles: Article[]): string {\n  const cslItems = articlesToCslJson(articles);\n  return JSON.stringify(cslItems, null, 2);\n}\n\n\nconst METADATA_FIELDS: (keyof Article)[] = [\n  'doi', 'pmid', 'arxivId', 'scopusId', 'ericId',\n  'abstract', 'publicationDate', 'journal', 'volume', 'issue', 'pages',\n];\n\nfunction countMetadataFields(article: Article): number {\n  let count = 0;\n  for (const field of METADATA_FIELDS) {\n    if (article[field] !== undefined && article[field] !== '') {\n      count++;\n    }\n  }\n  return count;\n}\n\nexport interface DeduplicationResult {\n  articles: Article[];\n  duplicatesRemoved: number;\n}\n\nexport function deduplicateArticles(articles: Article[]): DeduplicationResult {\n  // Map from identifier key to index in the unique array\n  const keyToIndex = new Map<string, number>();\n  const unique: Article[] = [];\n  let duplicatesRemoved = 0;\n\n  for (const article of articles) {\n    const keys = getArticleKeys(article);\n\n    if (keys.length === 0) {\n      // No identifiers - cannot deduplicate, keep the article\n      unique.push(article);\n      continue;\n    }\n\n    // Check if any identifier has been seen before\n    let existingIndex: number | undefined;\n    for (const key of keys) {\n      const idx = keyToIndex.get(key);\n      if (idx !== undefined) {\n        existingIndex = idx;\n        break;\n      }\n    }\n\n    if (existingIndex !== undefined) {\n      // Duplicate found - compare metadata richness\n      const existing = unique[existingIndex]!;\n      if (countMetadataFields(article) > countMetadataFields(existing)) {\n        // Replace with the richer record\n        unique[existingIndex] = article;\n        // Update all keys to point to the same index\n        const newKeys = getArticleKeys(article);\n        for (const key of newKeys) {\n          keyToIndex.set(key, existingIndex);\n        }\n      }\n      duplicatesRemoved++;\n    } else {\n      const index = unique.length;\n      unique.push(article);\n      // Map all identifiers to this index\n      for (const key of keys) {\n        keyToIndex.set(key, index);\n      }\n    }\n  }\n\n  return { articles: unique, duplicatesRemoved };\n}\n\nexport function filterArticles(articles: Article[], filter: ExportFilter): Article[] {\n  const hasYearFilter = filter.yearFrom !== undefined || filter.yearTo !== 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package/dist/cli/commands/query/init.d.ts.map

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package/dist/cli/commands/query/init.js

@@ -7,7 +7,8 @@ name: my_search
 description: ""
 
 query:
-  - field: title_abstract    # title, abstract, title_abstract, author, keyword, all
+  - id: concept-1             # Unique block identifier (for provider replacements)
+    field: title_abstract    # title, abstract, title_abstract, author, keyword, all
     terms:
       keywords:
         - "search term 1"
@@ -24,7 +25,8 @@ query:
     operator: OR             # How to combine terms within this block
 
   # Add more blocks — blocks are AND'd together
-  # - field: title_abstract
+  # - id: concept-2
+  #   field: title_abstract
   #   terms:
   #     keywords:
   #       - "another term"
@@ -40,12 +42,20 @@ query:
 #       - "Review"
 #       - "Comment"
 
-# overrides:                 # Optional: database-specific settings
+# providers:                 # Optional: per-database block replacements & filter additions
 #   pubmed:
-#     filters:
-#       publication_types:
-#         exclude:
-#           - "Letter"
+#     replaces:
+#       concept-1:           # Replace block by id
+#         field: keyword
+#         terms:
+#           mesh:
+#             - "MeSH Heading"
+#         operator: OR
+#     adds:
+#       filters:
+#         publication_types:
+#           exclude:
+#             - "Letter"
 `;
 function generateQueryTemplate() {
   return QUERY_TEMPLATE;

package/dist/cli/commands/query/init.js.map

@@ -1 +1 @@
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+{"version":3,"file":"init.js","sources":["../../../../src/cli/commands/query/init.ts"],"sourcesContent":["/**\n * Query init command implementation.\n *\n * Generates a skeleton YAML query file with helpful comments.\n */\nimport { writeFile as fsWriteFile, access } from \"node:fs/promises\";\nimport { dirname, join } from \"node:path\";\nimport { generateQueryJSONSchema } from \"../../../query/json-schema.js\";\n\n/**\n * The YAML template string with comments preserved.\n * This is a raw string (not generated by a YAML library) so comments are kept.\n */\nexport const QUERY_SCHEMA_FILENAME = \"query.schema.json\";\n\n// prettier-ignore\nconst QUERY_TEMPLATE =\n  `# yaml-language-server: $schema=./${QUERY_SCHEMA_FILENAME}\\n` +\n  \"name: my_search\\n\" +\n  \"description: \\\"\\\"\\n\" +\n  \"\\n\" +\n  \"query:\\n\" +\n  \"  - id: concept-1             # Unique block identifier (for provider replacements)\\n\" +\n  \"    field: title_abstract    # title, abstract, title_abstract, author, keyword, all\\n\" +\n  \"    terms:\\n\" +\n  \"      keywords:\\n\" +\n  \"        - \\\"search term 1\\\"\\n\" +\n  \"        - \\\"search term 2\\\"\\n\" +\n  \"      # mesh:                 # PubMed MeSH terms (optional)\\n\" +\n  \"      #   - \\\"MeSH Heading\\\"\\n\" +\n  \"      # eric:                 # ERIC Descriptors (optional, ERIC only)\\n\" +\n  \"      #   - \\\"ERIC Descriptor\\\"\\n\" +\n  \"      exclude: []             # Terms to exclude (NOT operator)\\n\" +\n  \"      # Tip: Use exclude to filter out false matches from short keywords/acronyms\\n\" +\n  \"      # exclude:\\n\" +\n  \"      #   - \\\"unwanted term\\\"\\n\" +\n  \"      #   - \\\"irrelevant topic\\\"\\n\" +\n  \"    operator: OR             # How to combine terms within this block\\n\" +\n  \"\\n\" +\n  \"  # Add more blocks — blocks are AND'd together\\n\" +\n  \"  # - id: concept-2\\n\" +\n  \"  #   field: title_abstract\\n\" +\n  \"  #   terms:\\n\" +\n  \"  #     keywords:\\n\" +\n  \"  #       - \\\"another term\\\"\\n\" +\n  \"  #   operator: OR\\n\" +\n  \"\\n\" +\n  \"# filters:                   # Optional: apply to all databases\\n\" +\n  \"#   year_from: 2020\\n\" +\n  \"#   year_to: 2026\\n\" +\n  \"#   language:\\n\" +\n  \"#     - en\\n\" +\n  \"#   publication_types:\\n\" +\n  \"#     exclude:\\n\" +\n  \"#       - \\\"Review\\\"\\n\" +\n  \"#       - \\\"Comment\\\"\\n\" +\n  \"\\n\" +\n  \"# providers:                 # Optional: per-database block replacements & filter additions\\n\" +\n  \"#   pubmed:\\n\" +\n  \"#     replaces:\\n\" +\n  \"#       concept-1:           # Replace block by id\\n\" +\n  \"#         field: keyword\\n\" +\n  \"#         terms:\\n\" +\n  \"#           mesh:\\n\" +\n  \"#             - \\\"MeSH Heading\\\"\\n\" +\n  \"#         operator: OR\\n\" +\n  \"#     adds:\\n\" +\n  \"#       filters:\\n\" +\n  \"#         publication_types:\\n\" +\n  \"#           exclude:\\n\" +\n  \"#             - \\\"Letter\\\"\\n\";\n\n/**\n * Generate the query template YAML string.\n *\n * @returns The YAML template string with comments\n */\nexport function generateQueryTemplate(): string {\n  return QUERY_TEMPLATE;\n}\n\n/**\n * Write the query template to a file or return it as a message.\n *\n * @param options - Output options\n * @param options.output - File path to write to (if omitted, returns template in message)\n * @param options.force - Whether to overwrite existing files\n * @returns Result with success status and message\n */\nexport async function writeQueryTemplate(options: {\n  output?: string;\n  force?: boolean;\n}): Promise<{ success: boolean; message: string }> {\n  const template = generateQueryTemplate();\n\n  if (!options.output) {\n    // No output file specified, return template as message\n    return { success: true, message: template };\n  }\n\n  // Check if file exists (unless force is set)\n  if (!options.force) {\n    try {\n      await access(options.output);\n      // File exists and force is not set\n      return {\n        success: false,\n        message: `File already exists: ${options.output}. Use --force to overwrite.`,\n      };\n    } catch {\n      // File does not exist, proceed\n    }\n  }\n\n  // Write to file\n  await fsWriteFile(options.output, template, \"utf-8\");\n\n  // Generate JSON Schema file alongside output\n  const schemaPath = join(dirname(options.output), QUERY_SCHEMA_FILENAME);\n  const jsonSchema = generateQueryJSONSchema();\n  await fsWriteFile(schemaPath, JSON.stringify(jsonSchema, null, 2) + \"\\n\", \"utf-8\");\n\n  return {\n    success: true,\n    message: `Template written to ${options.output}`,\n  };\n}\n"],"names":["fsWriteFile"],"mappings":";;;AAaO,MAAM,wBAAwB;AAGrC,MAAM,iBACJ,qCAAqC,qBAAqB;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA4DrD,SAAS,wBAAgC;AAC9C,SAAO;AACT;AAUA,eAAsB,mBAAmB,SAGU;AACjD,QAAM,WAAW,sBAAA;AAEjB,MAAI,CAAC,QAAQ,QAAQ;AAEnB,WAAO,EAAE,SAAS,MAAM,SAAS,SAAA;AAAA,EACnC;AAGA,MAAI,CAAC,QAAQ,OAAO;AAClB,QAAI;AACF,YAAM,OAAO,QAAQ,MAAM;AAE3B,aAAO;AAAA,QACL,SAAS;AAAA,QACT,SAAS,wBAAwB,QAAQ,MAAM;AAAA,MAAA;AAAA,IAEnD,QAAQ;AAAA,IAER;AAAA,EACF;AAGA,QAAMA,UAAY,QAAQ,QAAQ,UAAU,OAAO;AAGnD,QAAM,aAAa,KAAK,QAAQ,QAAQ,MAAM,GAAG,qBAAqB;AACtE,QAAM,aAAa,wBAAA;AACnB,QAAMA,UAAY,YAAY,KAAK,UAAU,YAAY,MAAM,CAAC,IAAI,MAAM,OAAO;AAEjF,SAAO;AAAA,IACL,SAAS;AAAA,IACT,SAAS,uBAAuB,QAAQ,MAAM;AAAA,EAAA;AAElD;"}

package/dist/cli/commands/query/inspect.d.ts

@@ -0,0 +1,36 @@
+import { QueryAST } from '../../../query/types.js';
+import { ProviderName } from '../../../providers/base/types.js';
+export interface BlockInspectRow {
+    id: string;
+    status: Partial<Record<ProviderName, 'default' | 'replaced'>>;
+}
+export interface FilterInspectRow {
+    filterKey: string;
+    values: Partial<Record<ProviderName, string>>;
+}
+export interface InspectResult {
+    name: string;
+    providers: ProviderName[];
+    blocks: BlockInspectRow[];
+    addedFilters: FilterInspectRow[];
+}
+export interface InspectCommandResult {
+    success: boolean;
+    error?: string;
+    result?: InspectResult;
+}
+/**
+ * Inspect a QueryAST to determine block resolution and filter additions per provider.
+ */
+export declare function inspectQuery(ast: QueryAST, enabledProviders: ProviderName[]): InspectResult;
+/**
+ * Format InspectResult as an aligned table string.
+ */
+export declare function formatInspectOutput(result: InspectResult): string;
+/**
+ * Run the inspect command on a query file.
+ */
+export declare function inspectQueryCommand(filePath: string, options?: {
+    providers?: ProviderName[];
+}): Promise<InspectCommandResult>;
+//# sourceMappingURL=inspect.d.ts.map

package/dist/cli/commands/query/inspect.d.ts.map

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