paper-manager 0.4.2 → 0.6.0

package/README.md

@@ -56,6 +56,7 @@ paper config list [--user]               # List all config
 ```bash
 paper kb create <name> -d <desc> [-e <model-id>] [--user]  # Create a knowledge base
 paper kb list [--all | --user]        # List knowledge bases
+paper kb update <id> [-n <name>] [-d <desc>]  # Update knowledge base metadata
 paper kb remove <id>                  # Remove a knowledge base
 paper kb query <id> <query-text>      # Query a knowledge base
 ```
@@ -63,7 +64,7 @@ paper kb query <id> <query-text>      # Query a knowledge base
 ### Literature (`paper lit`)
 
 ```bash
-paper lit add <kb-id> <file-path>     # Add a literature (PDF, TXT, MD, TEX, etc.)
+paper lit add <kb-id> <file-path>     # Add a literature (auto-extracts PDF metadata)
 paper lit remove <kb-id> <id>         # Remove a literature
 paper lit update <kb-id> <id> [opts]  # Update literature metadata
 paper lit list <kb-id>                # List literatures
@@ -73,6 +74,12 @@ paper lit note set <lit-id> <k> <v>   # Set a note
 paper lit note remove <lit-id> <key>  # Remove a note
 ```
 
+### Utilities (`paper util`)
+
+```bash
+paper util doi2bib <doi>             # Convert a DOI to BibTeX citation
+```
+
 ## Configuration
 
 See [Configuration Reference](docs/configuration.md) for all available config fields and detailed usage.

package/dist/commands/knowledge-base.js

@@ -81,6 +81,37 @@ export function createKnowledgeBaseCommand() {
         }
         log.count(results.length, results.length === 1 ? "knowledge base" : "knowledge bases");
     });
+    kb.command("update <id>")
+        .description("Update knowledge base metadata")
+        .option("-n, --name <name>", "New name")
+        .option("-d, --description <desc>", "New description")
+        .action((id, options) => {
+        if (options.name === undefined && options.description === undefined) {
+            log.error("At least one of --name or --description must be provided.");
+            process.exit(1);
+        }
+        const resolved = resolveKnowledgeBase(id);
+        if (!resolved) {
+            log.error(`Knowledge base not found: ${id}`);
+            process.exit(1);
+        }
+        const { scope } = resolved;
+        const kbOps = scope === "project" ? projectKb : userKb;
+        const input = {};
+        if (options.name !== undefined)
+            input.name = options.name;
+        if (options.description !== undefined)
+            input.description = options.description;
+        const updated = kbOps.updateKnowledgeBase(id, input);
+        if (!updated) {
+            log.error("Failed to update knowledge base.");
+            process.exit(1);
+        }
+        log.success(`Knowledge base updated: ${updated.id}`);
+        log.label("Name:", updated.name);
+        log.label("Description:", updated.description);
+        log.label("Scope:", scope);
+    });
     kb.command("remove <id>")
         .description("Remove a knowledge base and all its data")
         .action((id) => {

package/dist/commands/knowledge-base.js.map

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+{"version":3,"file":"knowledge-base.js","sourceRoot":"","sources":["../../src/commands/knowledge-base.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,MAAM,SAAS,CAAC;AAC9B,OAAO,KAAK,IAAI,MAAM,WAAW,CAAC;AAElC,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EACL,SAAS,EACT,WAAW,EACX,cAAc,EACd,iBAAiB,EACjB,cAAc,EACd,iBAAiB,GAClB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,KAAK,SAAS,MAAM,kCAAkC,CAAC;AAC9D,OAAO,KAAK,UAAU,MAAM,8BAA8B,CAAC;AAC3D,OAAO,KAAK,MAAM,MAAM,+BAA+B,CAAC;AACxD,OAAO,KAAK,OAAO,MAAM,2BAA2B,CAAC;AACrD,OAAO,EAAE,GAAG,EAAE,MAAM,cAAc,CAAC;AAEnC,OAAO,EAAE,gBAAgB,EAAE,MAAM,0BAA0B,CAAC;AAE5D,SAAS,oBAAoB,CAC3B,EAAU;IAEV,MAAM,GAAG,GAAG,SAAS,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC;IAC3C,IAAI,GAAG;QAAE,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC;IAC9C,MAAM,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC,EAAE,CAAC,CAAC;IACxC,IAAI,GAAG;QAAE,OAAO,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC;IAC3C,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,UAAU,CAAC,KAAyB;IAC3C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,iBAAiB,EAAE,CAAC,CAAC,CAAC,cAAc,EAAE,CAAC;AACtE,CAAC;AAED,MAAM,UAAU,0BAA0B;IACxC,MAAM,EAAE,GAAG,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,wBAAwB,CAAC,CAAC;IAEnE,EAAE,CAAC,OAAO,CAAC,eAAe,CAAC;SACxB,WAAW,CAAC,yBAAyB,CAAC;SACtC,cAAc,CAAC,0BAA0B,EAAE,4BAA4B,CAAC;SACxE,MAAM,CAAC,4BAA4B,EAAE,2BAA2B,CAAC;SACjE,MAAM,CAAC,QAAQ,EAAE,sBAAsB,CAAC;SACxC,MAAM,CACL,CACE,IAAY,EACZ,OAIC,EACD,EAAE;QACF,IAAI,gBAAgB,GAAG,OAAO,CAAC,cAAc,CAAC;QAC9C,IAAI,CAAC,gBAAgB,EAAE,CAAC;YACtB,MAAM,SAAS,GAAG,SAAS,CAAC,yBAAyB,CAAC,CAAC;YACvD,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,GAAG,CAAC,KAAK,CAAC,yDAAyD,CAAC,CAAC;gBACrE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;YAClB,CAAC;YACD,gBAAgB,GAAG,SAAS,CAAC;QAC/B,CAAC;QAED,+BAA+B;QAC/B,MAAM,MAAM,GAAG,SAAS,CAAC,iBAAiB,CAAC,CAAC;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC,gBAAgB,CAAC,EAAE,CAAC;YAChC,GAAG,CAAC,KAAK,CAAC,oBAAoB,gBAAgB,wBAAwB,CAAC,CAAC;YACxE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,mBAAmB,CAAC,CAAC,CAAC,SAAS,CAAC,mBAAmB,CAAC;QAEzF,MAAM,MAAM,GAAG,MAAM,CAAC;YACpB,IAAI;YACJ,WAAW,EAAE,OAAO,CAAC,WAAW;YAChC,gBAAgB;SACjB,CAAC,CAAC;QAEH,GAAG,CAAC,OAAO,CAAC,2BAA2B,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACpD,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;QAChC,GAAG,CAAC,KAAK,CAAC,QAAQ,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACzD,CAAC,CACF,CAAC;IAEJ,EAAE,CAAC,OAAO,CAAC,MAAM,CAAC;SACf,WAAW,CAAC,sBAAsB,CAAC;SACnC,MAAM,CAAC,QAAQ,EAAE,gCAAgC,CAAC;SAClD,MAAM,CAAC,OAAO,EAAE,oCAAoC,CAAC;SACrD,MAAM,CAAC,CAAC,OAA0C,EAAE,EAAE;QACrD,IAAI,OAAO,GAAqD,EAAE,CAAC;QAEnE,IAAI,OAAO,CAAC,IAAI,EAAE,CAAC;YACjB,OAAO,GAAG,MAAM,CAAC,kBAAkB,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC;QAC9E,CAAC;aAAM,CAAC;YACN,MAAM,UAAU,GAAG,SAAS,CAAC,kBAAkB,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,SAAS,EAAE,CAAC,CAAC,CAAC;YAC3F,MAAM,OAAO,GAAG,MAAM,CAAC,kBAAkB,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC;YAClF,OAAO,GAAG,CAAC,GAAG,UAAU,EAAE,GAAG,OAAO,CAAC,CAAC;QACxC,CAAC;QAED,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,GAAG,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;YACtC,OAAO;QACT,CAAC;QAED,KAAK,MAAM,EAAE,IAAI,OAAO,EAAE,CAAC;YACzB,GAAG,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACrC,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,CAAC,IAAI,CAAC,CAAC;YAC5B,GAAG,CAAC,KAAK,CAAC,cAAc,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC;YAC1C,GAAG,CAAC,KAAK,CAAC,QAAQ,EAAE,EAAE,CAAC,gBAAgB,CAAC,CAAC;YACzC,GAAG,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,CAAC,SAAS,CAAC,WAAW,EAAE,CAAC,CAAC;YAClD,GAAG,CAAC,OAAO,EAAE,CAAC;QAChB,CAAC;QACD,GAAG,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC;IACzF,CAAC,CAAC,CAAC;IAEL,EAAE,CAAC,OAAO,CAAC,aAAa,CAAC;SACtB,WAAW,CAAC,gCAAgC,CAAC;SAC7C,MAAM,CAAC,mBAAmB,EAAE,UAAU,CAAC;SACvC,MAAM,CAAC,0BAA0B,EAAE,iBAAiB,CAAC;SACrD,MAAM,CAAC,CAAC,EAAU,EAAE,OAAgD,EAAE,EAAE;QACvE,IAAI,OAAO,CAAC,IAAI,KAAK,SAAS,IAAI,OAAO,CAAC,WAAW,KAAK,SAAS,EAAE,CAAC;YACpE,GAAG,CAAC,KAAK,CAAC,2DAA2D,CAAC,CAAC;YACvE,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,MAAM,QAAQ,GAAG,oBAAoB,CAAC,EAAE,CAAC,CAAC;QAC1C,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,GAAG,CAAC,KAAK,CAAC,6BAA6B,EAAE,EAAE,CAAC,CAAC;YAC7C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,MAAM,EAAE,KAAK,EAAE,GAAG,QAAQ,CAAC;QAC3B,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC;QAEvD,MAAM,KAAK,GAA4C,EAAE,CAAC;QAC1D,IAAI,OAAO,CAAC,IAAI,KAAK,SAAS;YAAE,KAAK,CAAC,IAAI,GAAG,OAAO,CAAC,IAAI,CAAC;QAC1D,IAAI,OAAO,CAAC,WAAW,KAAK,SAAS;YAAE,KAAK,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAC;QAE/E,MAAM,OAAO,GAAG,KAAK,CAAC,mBAAmB,CAAC,EAAE,EAAE,KAAK,CAAC,CAAC;QACrD,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,GAAG,CAAC,KAAK,CAAC,kCAAkC,CAAC,CAAC;YAC9C,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,GAAG,CAAC,OAAO,CAAC,2BAA2B,OAAO,CAAC,EAAE,EAAE,CAAC,CAAC;QACrD,GAAG,CAAC,KAAK,CAAC,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,CAAC;QACjC,GAAG,CAAC,KAAK,CAAC,cAAc,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;QAC/C,GAAG,CAAC,KAAK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package/dist/commands/literature.js

@@ -9,7 +9,7 @@ import * as projectKb from "../db/project/knowledge-bases.js";
 import * as projectLit from "../db/project/literatures.js";
 import * as userKb from "../db/user/knowledge-bases.js";
 import * as userLit from "../db/user/literatures.js";
-import { extractContent } from "../extractor/index.js";
+import { extractContent, extractPdfMetadata } from "../extractor/index.js";
 import { log } from "../logger.js";
 import { createVectorStore, loadVectorStore } from "../vector-store/index.js";
 function resolveKnowledgeBase(id) {
@@ -49,19 +49,43 @@ export function createLiteratureCommand() {
             log.error(`File not found: ${absolutePath}`);
             process.exit(1);
         }
-        const title = options.title ?? path.basename(litPath, path.extname(litPath));
         log.info("Extracting content...");
         const docs = await extractContent(absolutePath);
         log.step(`Extracted ${String(docs.length)} pages.`);
+        // Extract PDF metadata if available
+        const isPdf = absolutePath.toLowerCase().endsWith(".pdf");
+        const pdfMeta = isPdf ? await extractPdfMetadata(absolutePath) : null;
+        if (pdfMeta) {
+            const hasAny = pdfMeta.title ?? pdfMeta.author ?? pdfMeta.doi ?? pdfMeta.subject;
+            if (hasAny || pdfMeta.keywords.length > 0) {
+                log.info("Extracted PDF metadata:");
+                if (pdfMeta.title)
+                    log.step(`Title: ${pdfMeta.title}`);
+                if (pdfMeta.author)
+                    log.step(`Author: ${pdfMeta.author}`);
+                if (pdfMeta.subject)
+                    log.step(`Subject: ${pdfMeta.subject}`);
+                if (pdfMeta.doi)
+                    log.step(`DOI: ${pdfMeta.doi}`);
+                if (pdfMeta.keywords.length > 0)
+                    log.step(`Keywords: ${pdfMeta.keywords.join(", ")}`);
+                if (pdfMeta.creationDate)
+                    log.step(`Created: ${pdfMeta.creationDate.toISOString()}`);
+                if (pdfMeta.creator)
+                    log.step(`Creator: ${pdfMeta.creator}`);
+            }
+        }
+        const title = options.title ?? pdfMeta?.title ?? path.basename(litPath, path.extname(litPath));
         // Create literature record
         const literature = litOps.createLiterature({
             title,
             titleTranslation: null,
-            author: null,
-            abstract: null,
+            author: pdfMeta?.author ?? null,
+            abstract: pdfMeta?.subject ?? null,
             summary: null,
-            keywords: [],
+            keywords: pdfMeta?.keywords ?? [],
             url: null,
+            doi: pdfMeta?.doi ?? null,
             notes: {},
             knowledgeBaseId: kbId,
         });
@@ -103,6 +127,14 @@ export function createLiteratureCommand() {
         bar.stop();
         log.success(`Literature added: ${literature.id}`);
         log.label("Title:", literature.title);
+        if (literature.author)
+            log.label("Author:", literature.author);
+        if (literature.abstract)
+            log.label("Abstract:", literature.abstract);
+        if (literature.doi)
+            log.label("DOI:", literature.doi);
+        if (literature.keywords.length > 0)
+            log.label("Keywords:", literature.keywords.join(", "));
     });
     // ─── lit remove ────────────────────────────────────────────
     lit
@@ -145,6 +177,7 @@ export function createLiteratureCommand() {
         .option("--abstract <abstract>", "Abstract")
         .option("--summary <summary>", "Summary")
         .option("--url <url>", "URL")
+        .option("--doi <doi>", "DOI")
         .option("--keywords <keywords>", "Keywords (comma-separated)")
         .action((kbId, id, options) => {
         const resolved = resolveKnowledgeBase(kbId);
@@ -153,21 +186,20 @@ export function createLiteratureCommand() {
             process.exit(1);
         }
         const litOps = getLitOps(resolved.scope);
-        const input = {};
-        if (options.title !== undefined)
-            input["title"] = options.title;
-        if (options.titleTranslation !== undefined)
-            input["titleTranslation"] = options.titleTranslation;
-        if (options.author !== undefined)
-            input["author"] = options.author;
-        if (options.abstract !== undefined)
-            input["abstract"] = options.abstract;
-        if (options.summary !== undefined)
-            input["summary"] = options.summary;
-        if (options.url !== undefined)
-            input["url"] = options.url;
-        if (options.keywords !== undefined)
-            input["keywords"] = options.keywords.split(",").map((k) => k.trim());
+        const input = {
+            ...(options.title !== undefined && { title: options.title }),
+            ...(options.titleTranslation !== undefined && {
+                titleTranslation: options.titleTranslation,
+            }),
+            ...(options.author !== undefined && { author: options.author }),
+            ...(options.abstract !== undefined && { abstract: options.abstract }),
+            ...(options.summary !== undefined && { summary: options.summary }),
+            ...(options.url !== undefined && { url: options.url }),
+            ...(options.doi !== undefined && { doi: options.doi }),
+            ...(options.keywords !== undefined && {
+                keywords: options.keywords.split(",").map((k) => k.trim()),
+            }),
+        };
         const updated = litOps.updateLiterature(id, input);
         if (!updated) {
             log.error(`Literature not found: ${id}`);
@@ -300,7 +332,10 @@ function printLiterature(lit) {
         log.label("Keywords:", lit.keywords.join(", "));
     if (lit.url)
         log.label("URL:", lit.url);
-    log.label("Knowledge Base:", lit.knowledgeBaseId);
+    if (lit.doi)
+        log.label("DOI:", lit.doi);
+    if (lit.knowledgeBaseId)
+        log.label("Knowledge Base:", lit.knowledgeBaseId);
     log.label("Created:", lit.createdAt.toISOString());
     log.label("Updated:", lit.updatedAt.toISOString());
     const noteEntries = Object.entries(lit.notes);

package/dist/commands/literature.js.map

@@ -1 +1 @@
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package/dist/commands/util.d.ts

@@ -0,0 +1,2 @@
+import { Command } from "commander";
+export declare function createUtilCommand(): Command;

package/dist/commands/util.js

@@ -0,0 +1,24 @@
+import { Command } from "commander";
+import { log } from "../logger.js";
+export function createUtilCommand() {
+    const util = new Command("util").description("Utility commands");
+    util
+        .command("doi2bib <doi>")
+        .description("Convert a DOI to BibTeX citation")
+        .action(async (doi) => {
+        const normalizedDoi = doi.replace(/^https?:\/\/doi\.org\//, "");
+        const url = `https://doi.org/${encodeURIComponent(normalizedDoi)}`;
+        const response = await fetch(url, {
+            headers: { Accept: "application/x-bibtex" },
+            redirect: "follow",
+        });
+        if (!response.ok) {
+            log.error(`Failed to resolve DOI: ${normalizedDoi} (HTTP ${String(response.status)})`);
+            process.exit(1);
+        }
+        const bibtex = await response.text();
+        log.plain(bibtex);
+    });
+    return util;
+}
+//# sourceMappingURL=util.js.map

package/dist/commands/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/commands/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAEpC,OAAO,EAAE,GAAG,EAAE,MAAM,cAAc,CAAC;AAEnC,MAAM,UAAU,iBAAiB;IAC/B,MAAM,IAAI,GAAG,IAAI,OAAO,CAAC,MAAM,CAAC,CAAC,WAAW,CAAC,kBAAkB,CAAC,CAAC;IAEjE,IAAI;SACD,OAAO,CAAC,eAAe,CAAC;SACxB,WAAW,CAAC,kCAAkC,CAAC;SAC/C,MAAM,CAAC,KAAK,EAAE,GAAW,EAAE,EAAE;QAC5B,MAAM,aAAa,GAAG,GAAG,CAAC,OAAO,CAAC,wBAAwB,EAAE,EAAE,CAAC,CAAC;QAChE,MAAM,GAAG,GAAG,mBAAmB,kBAAkB,CAAC,aAAa,CAAC,EAAE,CAAC;QAEnE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;YAChC,OAAO,EAAE,EAAE,MAAM,EAAE,sBAAsB,EAAE;YAC3C,QAAQ,EAAE,QAAQ;SACnB,CAAC,CAAC;QAEH,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;YACjB,GAAG,CAAC,KAAK,CAAC,0BAA0B,aAAa,UAAU,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACvF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QACrC,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IACpB,CAAC,CAAC,CAAC;IAEL,OAAO,IAAI,CAAC;AACd,CAAC"}

package/dist/db/index.d.ts

@@ -1,9 +1,7 @@
 import type BetterSqlite3 from "better-sqlite3";
-import type { KnowledgeBaseMetadata, LiteratureMetadata } from "../types/index.js";
-export declare function isRecord(value: unknown): value is Record<string, unknown>;
-export declare function dbRowToKnowledgeBase(row: unknown): KnowledgeBaseMetadata;
-export declare function dbRowToLiterature(row: unknown): LiteratureMetadata;
+import type { BetterSQLite3Database } from "drizzle-orm/better-sqlite3";
+export type AppDatabase = BetterSQLite3Database;
 export declare function openDatabase(dbPath: string): BetterSqlite3.Database;
 export declare function initializeDatabase(db: BetterSqlite3.Database): void;
-export declare function getUserDb(): BetterSqlite3.Database;
-export declare function getProjectDb(): BetterSqlite3.Database;
+export declare function getUserDb(): AppDatabase;
+export declare function getProjectDb(): AppDatabase;

package/dist/db/index.js

@@ -1,46 +1,9 @@
 import * as fs from "node:fs";
 import * as path from "node:path";
 import Database from "better-sqlite3";
+import { drizzle } from "drizzle-orm/better-sqlite3";
 import { getProjectDataDir, getUserDataDir } from "../config/index.js";
-import { KnowledgeBaseMetadataSchema, LiteratureMetadataSchema } from "../types/index.js";
 import { CREATE_KNOWLEDGE_BASES_TABLE, CREATE_LITERATURES_TABLE } from "./schema.js";
-// ─── Type Guard ─────────────────────────────────────────────
-export function isRecord(value) {
-    return typeof value === "object" && value !== null && !Array.isArray(value);
-}
-// ─── Row Converters ─────────────────────────────────────────
-export function dbRowToKnowledgeBase(row) {
-    if (!isRecord(row)) {
-        throw new Error("Invalid database row: expected an object");
-    }
-    return KnowledgeBaseMetadataSchema.parse({
-        id: row["id"],
-        name: row["name"],
-        description: row["description"],
-        embeddingModelId: row["embedding_model_id"],
-        createdAt: new Date(Number(row["created_at"])),
-        updatedAt: new Date(Number(row["updated_at"])),
-    });
-}
-export function dbRowToLiterature(row) {
-    if (!isRecord(row)) {
-        throw new Error("Invalid database row: expected an object");
-    }
-    return LiteratureMetadataSchema.parse({
-        id: row["id"],
-        title: row["title"],
-        titleTranslation: row["title_translation"] ?? null,
-        author: row["author"] ?? null,
-        abstract: row["abstract"] ?? null,
-        summary: row["summary"] ?? null,
-        keywords: JSON.parse(typeof row["keywords"] === "string" ? row["keywords"] : "[]"),
-        url: row["url"] ?? null,
-        notes: JSON.parse(typeof row["notes"] === "string" ? row["notes"] : "{}"),
-        knowledgeBaseId: row["knowledge_base_id"],
-        createdAt: new Date(Number(row["created_at"])),
-        updatedAt: new Date(Number(row["updated_at"])),
-    });
-}
 // ─── Database Connection ────────────────────────────────────
 export function openDatabase(dbPath) {
     const dir = path.dirname(dbPath);
@@ -53,6 +16,28 @@ export function openDatabase(dbPath) {
 export function initializeDatabase(db) {
     db.exec(CREATE_KNOWLEDGE_BASES_TABLE);
     db.exec(CREATE_LITERATURES_TABLE);
+    migrateDatabase(db);
+}
+// ─── Migrations ─────────────────────────────────────────────
+const MIGRATIONS = [
+    // v0 → v1: add doi column to literatures
+    (db) => {
+        const columns = db.pragma("table_info(literatures)");
+        if (!columns.some((c) => c.name === "doi")) {
+            db.exec("ALTER TABLE literatures ADD COLUMN doi TEXT");
+        }
+    },
+];
+function migrateDatabase(db) {
+    const currentVersion = db.pragma("user_version", { simple: true }) ?? 0;
+    if (currentVersion >= MIGRATIONS.length)
+        return;
+    db.transaction(() => {
+        for (let i = currentVersion; i < MIGRATIONS.length; i++) {
+            MIGRATIONS[i](db);
+        }
+        db.pragma(`user_version = ${String(MIGRATIONS.length)}`);
+    })();
 }
 // ─── Singleton Connections ──────────────────────────────────
 let userDb = null;
@@ -60,16 +45,18 @@ let projectDb = null;
 export function getUserDb() {
     if (!userDb) {
         const dbPath = path.join(getUserDataDir(), "papers.db");
-        userDb = openDatabase(dbPath);
-        initializeDatabase(userDb);
+        const client = openDatabase(dbPath);
+        initializeDatabase(client);
+        userDb = drizzle(client);
     }
     return userDb;
 }
 export function getProjectDb() {
     if (!projectDb) {
         const dbPath = path.join(getProjectDataDir(), "papers.db");
-        projectDb = openDatabase(dbPath);
-        initializeDatabase(projectDb);
+        const client = openDatabase(dbPath);
+        initializeDatabase(client);
+        projectDb = drizzle(client);
     }
     return projectDb;
 }

package/dist/db/index.js.map

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package/dist/db/index.test.js

@@ -1,79 +1,32 @@
 import { describe, expect, it } from "vitest";
-import { dbRowToKnowledgeBase, dbRowToLiterature, isRecord } from "./index.js";
-// ─── isRecord ────────────────────────────────────────────────
-describe("isRecord", () => {
-    it("returns true for plain objects", () => {
-        expect(isRecord({})).toBe(true);
-        expect(isRecord({ a: 1 })).toBe(true);
-    });
-    it("returns false for arrays", () => {
-        expect(isRecord([])).toBe(false);
-        expect(isRecord([1, 2])).toBe(false);
-    });
-    it("returns false for primitives and null", () => {
-        expect(isRecord(null)).toBe(false);
-        expect(isRecord(undefined)).toBe(false);
-        expect(isRecord(42)).toBe(false);
-        expect(isRecord("string")).toBe(false);
-        expect(isRecord(true)).toBe(false);
+import { initializeDatabase, openDatabase } from "./index.js";
+// ─── openDatabase ────────────────────────────────────────────
+describe("openDatabase", () => {
+    it("opens an in-memory database with foreign keys enabled", () => {
+        const db = openDatabase(":memory:");
+        // WAL mode silently falls back to "memory" for in-memory databases
+        expect(db.pragma("foreign_keys", { simple: true })).toBe(1);
+        db.close();
     });
 });
-// ─── dbRowToKnowledgeBase ────────────────────────────────────
-describe("dbRowToKnowledgeBase", () => {
-    const validRow = {
-        id: "550e8400-e29b-41d4-a716-446655440000",
-        name: "Test KB",
-        description: "A description",
-        embedding_model_id: "model-1",
-        created_at: 1700000000000,
-        updated_at: 1700000000000,
-    };
-    it("converts a valid DB row to KnowledgeBaseMetadata", () => {
-        const result = dbRowToKnowledgeBase(validRow);
-        expect(result.id).toBe(validRow.id);
-        expect(result.name).toBe("Test KB");
-        expect(result.embeddingModelId).toBe("model-1");
-        expect(result.createdAt).toBeInstanceOf(Date);
-        expect(result.createdAt.getTime()).toBe(1700000000000);
-    });
-    it("throws on non-object input", () => {
-        expect(() => dbRowToKnowledgeBase(null)).toThrow("Invalid database row");
-        expect(() => dbRowToKnowledgeBase("string")).toThrow("Invalid database row");
-        expect(() => dbRowToKnowledgeBase([])).toThrow("Invalid database row");
-    });
-});
-// ─── dbRowToLiterature ───────────────────────────────────────
-describe("dbRowToLiterature", () => {
-    const validRow = {
-        id: "550e8400-e29b-41d4-a716-446655440000",
-        title: "A Paper",
-        title_translation: null,
-        author: "Alice",
-        abstract: "This paper...",
-        summary: null,
-        keywords: '["ai","ml"]',
-        url: null,
-        notes: '{"read":"yes"}',
-        knowledge_base_id: "550e8400-e29b-41d4-a716-446655440000",
-        created_at: 1700000000000,
-        updated_at: 1700000000000,
-    };
-    it("converts a valid DB row with JSON fields", () => {
-        const result = dbRowToLiterature(validRow);
-        expect(result.title).toBe("A Paper");
-        expect(result.author).toBe("Alice");
-        expect(result.keywords).toEqual(["ai", "ml"]);
-        expect(result.notes).toEqual({ read: "yes" });
-        expect(result.knowledgeBaseId).toBe(validRow.knowledge_base_id);
-    });
-    it("handles missing keywords/notes with defaults", () => {
-        const row = { ...validRow, keywords: undefined, notes: undefined };
-        const result = dbRowToLiterature(row);
-        expect(result.keywords).toEqual([]);
-        expect(result.notes).toEqual({});
-    });
-    it("throws on non-object input", () => {
-        expect(() => dbRowToLiterature(42)).toThrow("Invalid database row");
+// ─── initializeDatabase ──────────────────────────────────────
+describe("initializeDatabase", () => {
+    it("creates knowledge_bases and literatures tables", () => {
+        const db = openDatabase(":memory:");
+        initializeDatabase(db);
+        const tables = db
+            .prepare("SELECT name FROM sqlite_master WHERE type = 'table' ORDER BY name")
+            .all();
+        const tableNames = tables.map((t) => t.name);
+        expect(tableNames).toContain("knowledge_bases");
+        expect(tableNames).toContain("literatures");
+        db.close();
+    });
+    it("is idempotent — can be called multiple times", () => {
+        const db = openDatabase(":memory:");
+        initializeDatabase(db);
+        expect(() => initializeDatabase(db)).not.toThrow();
+        db.close();
     });
 });
 //# sourceMappingURL=index.test.js.map

package/dist/db/index.test.js.map

@@ -1 +1 @@
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package/dist/db/operations/knowledge-bases.d.ts

@@ -1,10 +1,11 @@
-import type BetterSqlite3 from "better-sqlite3";
-import type { KnowledgeBaseMetadata } from "../../types/index.js";
-export declare function createKnowledgeBase(db: BetterSqlite3.Database, input: {
+import type { KnowledgeBaseMetadata, UpdateKnowledgeBaseInput } from "../../types/index.js";
+import type { AppDatabase } from "../index.js";
+export declare function createKnowledgeBase(db: AppDatabase, input: {
     name: string;
     description: string;
     embeddingModelId: string;
 }): KnowledgeBaseMetadata;
-export declare function getKnowledgeBase(db: BetterSqlite3.Database, id: string): KnowledgeBaseMetadata | null;
-export declare function listKnowledgeBases(db: BetterSqlite3.Database): KnowledgeBaseMetadata[];
-export declare function deleteKnowledgeBase(db: BetterSqlite3.Database, id: string): boolean;
+export declare function getKnowledgeBase(db: AppDatabase, id: string): KnowledgeBaseMetadata | null;
+export declare function listKnowledgeBases(db: AppDatabase): KnowledgeBaseMetadata[];
+export declare function updateKnowledgeBase(db: AppDatabase, id: string, input: UpdateKnowledgeBaseInput): KnowledgeBaseMetadata | null;
+export declare function deleteKnowledgeBase(db: AppDatabase, id: string): boolean;