@ncukondo/search-hub 0.12.1 → 0.12.2

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

@@ -1 +1 @@
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 reviewsChanged = true;\n          }\n        }\n      }\n\n      if (reviewsChanged) {\n        await writeFile(reviewsPath, stringifyYaml(reviewFile), 'utf-8');\n      }\n    } catch {\n      // No reviews.yaml - that's fine\n    }\n  }\n\n  return {\n    synced: totalSynced,\n    articlesUpdated: articlesWithChanges.size,\n    entries: syncEntries,\n    ...(dryRun && { dryRun: true }),\n  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package/dist/cli/commands/review/types.d.ts

@@ -1,4 +1,4 @@
-import { ArticleFulltextRef } from '../../../fulltext/types.js';
+import { ArticleFulltextRef } from '@ncukondo/academic-fulltext';
 export type ReviewDecision = 'include' | 'exclude' | 'uncertain';
 /**
  * Basis of the review decision (what information was used)

package/dist/cli/commands/review/types.d.ts.map

@@ -1 +1 @@
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package/dist/cli/commands/review/types.js.map

@@ -1 +1 @@
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+{"version":3,"file":"types.js","sources":["../../../../src/cli/commands/review/types.ts"],"sourcesContent":["/**\n * Review workflow types for article assessment tracking\n */\n\nimport type { ArticleFulltextRef } from '@ncukondo/academic-fulltext';\n\nexport type ReviewDecision = 'include' | 'exclude' | 'uncertain';\n\n/**\n * Basis of the review decision (what information was used)\n */\nexport type ReviewBasis = 'title' | 'abstract' | 'fulltext';\n\n/**\n * Individual assessment of an article by a reviewer\n */\nexport interface Review {\n  /** Reviewer identifier: \"human:name\" or \"ai:name\" */\n  reviewer: string;\n  /** Assessment decision */\n  decision?: ReviewDecision;\n  /** Basis of the decision (what information was used) */\n  basis?: ReviewBasis;\n  /** Optional comment or reason */\n  comment?: string;\n  /** ISO 8601 timestamp (optional - auto-assigned on merge if not provided) */\n  timestamp?: string;\n}\n\n/**\n * Source information for merged duplicates\n */\nexport interface MergedSource {\n  source: string;\n  pmid?: string;\n  doi?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n}\n\n/**\n * Article entry with identifiers, bibliographic info, and reviews\n */\nexport interface ArticleEntry {\n  // Identifiers (at least one required for matching)\n  doi?: string;\n  pmid?: string;\n  scopusId?: string;\n  arxivId?: string;\n  ericId?: string;\n\n  // Bibliographic info (for reviewer reference)\n  title: string;\n  authors?: string;\n  year?: string;\n  abstract?: string;\n\n  // Deduplication tracking\n  mergedFrom?: MergedSource[];\n\n  // Review data\n  reviews: Review[];\n  /** Historical reviews (only in extracted ReviewFiles, never in master file) */\n  reviewHistory?: Review[];\n  finalDecision?: 'include' | 'exclude' | null;\n\n  // Fulltext reference (set by fulltext init/sync)\n  fulltext?: ArticleFulltextRef;\n}\n\n/**\n * Top-level structure of the reviews.yaml file\n */\nexport interface ReviewerRecord {\n  name: string;\n  basis: ReviewBasis;\n}\n\nexport interface ReviewFile {\n  sessionId: string;\n  /** Path to inclusion criteria file */\n  criteria?: string;\n  /** Reviewer identifier (only in extracted ReviewFiles) */\n  reviewer?: string;\n  /** Basis level for screening (only in extracted ReviewFiles) */\n  basis?: ReviewBasis;\n  articles: ArticleEntry[];\n  /** Registry of reviewers who participated at each basis level */\n  reviewers?: ReviewerRecord[];\n}\n\n/**\n * Work file article entry for AI agent workflow\n */\n/** @deprecated Use ReviewFile format with reviews[] instead. 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Kept for backward compatibility. */\nexport interface WorkFile {\n  sessionId: string;\n  basis: ReviewBasis;\n  reviewer: string;\n  articles: WorkFileArticle[];\n}\n\n/**\n * Basis priority rank: fulltext > abstract > title > undefined\n */\nconst BASIS_RANK: Record<string, number> = {\n  title: 1,\n  abstract: 2,\n  fulltext: 3,\n};\n\nexport function basisRank(basis: ReviewBasis | undefined): number {\n  if (basis === undefined) return 0;\n  return BASIS_RANK[basis] ?? 0;\n}\n\n/**\n * Review status classification (7-state model)\n */\nexport type ReviewStatus =\n  | 'pending'\n  | 'incomplete'\n  | 'uncertain'\n  | 'agreed-include'\n  | 'agreed-exclude'\n  | 'conflicting'\n  | 'finalized';\n\n/**\n * Classify the review status of an article entry\n *\n * Classification logic (in order):\n * 1. finalDecision set?           → finalized\n * 2. No reviews?                  → pending\n * 3. Registered reviewer missing? → incomplete\n * 4. include AND exclude present? → conflicting\n * 5. Any uncertain?               → uncertain\n * 6. All include?                 → agreed-include\n * 7. All exclude?                 → agreed-exclude\n */\nexport function classifyStatus(\n  entry: ArticleEntry,\n  registeredReviewers?: ReviewerRecord[]\n): ReviewStatus {\n  // 1. Finalized takes precedence\n  if (entry.finalDecision !== undefined && entry.finalDecision !== null) {\n    return 'finalized';\n  }\n\n  // No reviews = pending (reviews can be null from YAML parsing with only comments)\n  const reviews = entry.reviews ?? [];\n  if (reviews.length === 0) {\n    return 'pending';\n  }\n\n  // 3. Check for incomplete (registered reviewer missing)\n  // Only check reviewers whose registered basis ≤ article's highest reviewed basis\n  if (registeredReviewers && registeredReviewers.length > 0) {\n    const reviewerNames = new Set(reviews.map((r) => r.reviewer));\n    let highestReviewedRank = 0;\n    for (const r of reviews) {\n      highestReviewedRank = Math.max(highestReviewedRank, basisRank(r.basis));\n    }\n    // When reviews have no basis (legacy), check all registered reviewers\n    const applicableReviewers = highestReviewedRank === 0\n      ? registeredReviewers\n      : registeredReviewers.filter(\n          (reg) => basisRank(reg.basis) <= highestReviewedRank\n        );\n    const hasAllReviewers = applicableReviewers.every((reg) =>\n      reviewerNames.has(reg.name)\n    );\n    if (applicableReviewers.length > 0 && !hasAllReviewers) {\n      return 'incomplete';\n    }\n  }\n\n  // Get reviews that have decisions\n  const reviewsWithDecisions = reviews.filter((r) => r.decision !== undefined);\n\n  if (reviewsWithDecisions.length === 0) {\n    // All reviews lack a decision — treat as pending\n    return 'pending';\n  }\n\n  // Basis-priority resolution:\n  // \"uncertain\" at a lower basis means \"need more info\" (escalate).\n  // A definitive decision at a higher basis resolves that uncertainty.\n  //\n  // Algorithm:\n  // 1. 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package/dist/config/schema.d.ts

@@ -103,6 +103,8 @@ export declare const ConfigSchema: z.ZodObject<{
         sources: z.ZodDefault<z.ZodObject<{
             unpaywall_email: z.ZodDefault<z.ZodString>;
             core_api_key: z.ZodDefault<z.ZodString>;
+            ncbi_email: z.ZodDefault<z.ZodString>;
+            ncbi_tool: z.ZodDefault<z.ZodString>;
             prefer_sources: z.ZodDefault<z.ZodArray<z.ZodString>>;
         }, z.core.$strip>>;
         download: z.ZodDefault<z.ZodObject<{

package/dist/config/schema.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../src/config/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAaxB;;;GAGG;AACH,eAAO,MAAM,oBAAoB;;;;;;;;;iBAc/B,CAAC;AAEH,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AASlE;;;GAGG;AACH,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA8GvB,CAAC;AAEH,MAAM,MAAM,MAAM,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,YAAY,CAAC,CAAC"}

package/dist/config/schema.js

@@ -55,10 +55,14 @@ const ConfigSchema = z.object({
     sources: z.object({
       unpaywall_email: z.string().default(""),
       core_api_key: z.string().default(""),
+      ncbi_email: z.string().default(""),
+      ncbi_tool: z.string().default("search-hub"),
       prefer_sources: z.array(z.string()).default(["pmc", "arxiv", "unpaywall", "core"])
     }).default(() => ({
       unpaywall_email: "",
       core_api_key: "",
+      ncbi_email: "",
+      ncbi_tool: "search-hub",
       prefer_sources: ["pmc", "arxiv", "unpaywall", "core"]
     })),
     download: z.object({
@@ -75,6 +79,8 @@ const ConfigSchema = z.object({
     sources: {
       unpaywall_email: "",
       core_api_key: "",
+      ncbi_email: "",
+      ncbi_tool: "search-hub",
       prefer_sources: ["pmc", "arxiv", "unpaywall", "core"]
     },
     download: {

package/dist/config/schema.js.map

@@ -1 +1 @@
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z.number().int().positive().default(PROVIDER_DEFAULTS.max_results),\n  inst_token: z.string().default(''),\n});\n\nexport type ProviderConfig = z.infer<typeof ProviderConfigSchema>;\n\n/**\n * Get default provider config object.\n */\nfunction getDefaultProviderConfig(): ProviderConfig {\n  return ProviderConfigSchema.parse({});\n}\n\n/**\n * Main configuration schema for search-hub.\n * All fields have defaults, so an empty object is valid input.\n */\nexport const ConfigSchema = z.object({\n  session: z\n    .object({\n      // Empty string means use platform default (resolved in loader.ts)\n      directory: z.string().default(''),\n    })\n    .default(() => ({ directory: '' })),\n\n  log: z\n    .object({\n      level: z.enum(['debug', 'info', 'warn', 'error']).default('info'),\n    })\n    .default(() => ({ level: 'info' as const })),\n\n  output: z\n    .object({\n      color: z.boolean().default(true),\n      progress_bar: z.boolean().default(true),\n    })\n    .default(() => ({ color: true, progress_bar: true })),\n\n  providers: z\n    .object({\n      pubmed: ProviderConfigSchema.default(getDefaultProviderConfig),\n      eric: ProviderConfigSchema.default(getDefaultProviderConfig),\n      arxiv: ProviderConfigSchema.default(getDefaultProviderConfig),\n      scopus: ProviderConfigSchema.default(getDefaultProviderConfig),\n      wos: ProviderConfigSchema.default(getDefaultProviderConfig),\n      embase: ProviderConfigSchema.default(getDefaultProviderConfig),\n    })\n    .default(() => ({\n      pubmed: getDefaultProviderConfig(),\n      eric: getDefaultProviderConfig(),\n      arxiv: getDefaultProviderConfig(),\n      scopus: getDefaultProviderConfig(),\n      wos: getDefaultProviderConfig(),\n      embase: getDefaultProviderConfig(),\n    })),\n\n  fulltext: z\n    .object({\n      enabled: z.boolean().default(true),\n      auto_convert_markdown: z.boolean().default(true),\n      auto_attach_on_register: z.boolean().default(true),\n      sources: z\n     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package/dist/{fulltext → integration}/attach-shared.d.ts

@@ -1,5 +1,5 @@
-import { FulltextMeta } from './types.js';
-import { FulltextAttachResult } from '../integration/types.js';
+import { FulltextMeta } from '@ncukondo/academic-fulltext';
+import { FulltextAttachResult } from './types.js';
 /** Files we try to attach, in priority order. */
 export declare const ATTACHABLE_FILES: readonly ["fulltext.pdf", "fulltext.md"];
 /**

package/dist/integration/attach-shared.d.ts.map

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package/dist/integration/attach-shared.js.map

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

@@ -1,6 +1,6 @@
 import { join } from "node:path";
 import { refFulltextAttach } from "./ref-cli.js";
-import { processFulltextEntries } from "../fulltext/attach-shared.js";
+import { processFulltextEntries } from "./attach-shared.js";
 function extractDoi(source) {
   if (source.startsWith("10.")) return source;
   if (source.startsWith("doi:")) return source.slice(4);

package/dist/integration/fulltext-attach.js.map

@@ -1 +1 @@
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package/dist/{fulltext → node_modules/@ncukondo/academic-fulltext/dist}/citation-key.js

@@ -1,5 +1,5 @@
-import anyAscii from "../node_modules/any-ascii/any-ascii.js";
 import { randomUUID } from "node:crypto";
+import anyAscii from "../../../any-ascii/any-ascii.js";
 function collisionSuffix(index) {
   let result = "";
   let n = index;

package/dist/node_modules/@ncukondo/academic-fulltext/dist/citation-key.js.map

@@ -0,0 +1 @@
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