paper-manager 0.10.4 → 0.11.1

package/README.md

@@ -55,22 +55,22 @@ 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
+paper kb list [--all | --user] [--json] [--jq <expr>]  # 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> [--json] [--jq <expr>]  # Query a knowledge base
 ```
 
 ### Literature (`paper lit`)
 
 ```bash
-paper lit add <kb-id> <file-path>     # Add a literature (auto-extracts PDF metadata)
+paper lit add <kb-id> <file-path> [-f] # Add a literature (auto-extracts PDF metadata, rejects duplicate DOI)
 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
-paper lit search <kb-id> [opts]       # Search literatures by metadata (--title/--author/--keyword/--doi)
-paper lit show <kb-id> <id>           # Show literature details
-paper lit note list <lit-id>          # List notes
+paper lit list <kb-id> [--json] [--jq <expr>]       # List literatures
+paper lit search <kb-id> [opts] [--json] [--jq <expr>]  # Search literatures by metadata
+paper lit show <kb-id> <id> [--json] [--jq <expr>]  # Show literature details
+paper lit note list <lit-id> [--json] [--jq <expr>]  # List notes
 paper lit note set <lit-id> <k> <v>   # Set a note
 paper lit note remove <lit-id> <key>  # Remove a note
 ```
@@ -79,7 +79,7 @@ paper lit note remove <lit-id> <key>  # Remove a note
 
 ```bash
 paper util doi2bib <doi>             # Convert a DOI to BibTeX citation
-paper util pdf-meta <file> [--json]  # Extract metadata from a PDF file
+paper util pdf-meta <file> [--json] [--jq <expr>]  # Extract metadata from a PDF file
 ```
 
 ## Configuration

package/dist/commands/knowledge-base.js

@@ -9,6 +9,7 @@ import * as userLit from "../db/user/literatures.js";
 import { removeImageDir } from "../extractor/markdown.js";
 import { log } from "../logger.js";
 import { queryVectorStore } from "../vector-store/index.js";
+import { outputJson } from "./output.js";
 function resolveKnowledgeBase(id) {
     const pkb = projectKb.getKnowledgeBase(id);
     if (pkb)
@@ -59,6 +60,7 @@ export function createKnowledgeBaseCommand() {
         .option("--user", "List user knowledge bases only")
         .option("--all", "List all knowledge bases (default)")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action((options) => {
         let results = [];
         if (options.user) {
@@ -70,16 +72,16 @@ export function createKnowledgeBaseCommand() {
             results = [...projectKbs, ...userKbs];
         }
         if (results.length === 0) {
-            if (options.json) {
-                log.plain("[]");
+            if (options.json || options.jq) {
+                outputJson([], options.jq);
             }
             else {
                 log.info("No knowledge bases found.");
             }
             return;
         }
-        if (options.json) {
-            log.plain(JSON.stringify(results, null, 2));
+        if (options.json || options.jq) {
+            outputJson(results, options.jq);
             return;
         }
         for (const kb of results) {
@@ -164,6 +166,7 @@ export function createKnowledgeBaseCommand() {
         .description("Query a knowledge base")
         .option("-k, --top-k <number>", "Number of results", "5")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action(async (id, queryText, options) => {
         const resolved = resolveKnowledgeBase(id);
         if (!resolved) {
@@ -181,19 +184,19 @@ export function createKnowledgeBaseCommand() {
         const k = parseInt(options.topK, 10);
         const results = await queryVectorStore(modelConfig, vectorDir, queryText, k);
         if (results.length === 0) {
-            if (options.json) {
-                log.plain("[]");
+            if (options.json || options.jq) {
+                outputJson([], options.jq);
             }
             else {
                 log.info("No results found.");
             }
             return;
         }
-        if (options.json) {
+        if (options.json || options.jq) {
             const output = results
                 .filter((doc) => doc != null)
                 .map((doc) => ({ pageContent: doc.pageContent, metadata: doc.metadata }));
-            log.plain(JSON.stringify(output, null, 2));
+            outputJson(output, options.jq);
             return;
         }
         for (let i = 0; i < results.length; i++) {

package/dist/commands/literature.js

@@ -13,6 +13,7 @@ import { convertPdfToMarkdown, isOpendataLoaderAvailable, removeImageDir, saveCo
 import { log } from "../logger.js";
 import { splitDocuments } from "../text-splitter.js";
 import { addDocuments, createVectorStore } from "../vector-store/index.js";
+import { outputJson } from "./output.js";
 function resolveKnowledgeBase(id) {
     const pkb = projectKb.getKnowledgeBase(id);
     if (pkb)
@@ -35,6 +36,7 @@ export function createLiteratureCommand() {
         .command("add <knowledge-base-id> <lit-path>")
         .description("Add a literature from a file (PDF, TXT, MD, TEX, etc.)")
         .option("-t, --title <title>", "Literature title")
+        .option("-f, --force", "Force add even if a literature with the same DOI already exists")
         .action(async (kbId, litPath, options) => {
         const resolved = resolveKnowledgeBase(kbId);
         if (!resolved) {
@@ -76,6 +78,15 @@ export function createLiteratureCommand() {
                     log.step(`Creator: ${pdfMeta.creator}`);
             }
         }
+        // Check for duplicate DOI in the knowledge base
+        if (pdfMeta?.doi && !options.force) {
+            const existing = litOps.findLiteratureByDoi(kbId, pdfMeta.doi);
+            if (existing) {
+                log.error(`A literature with DOI "${pdfMeta.doi}" already exists in this knowledge base: ${existing.id} (${existing.title})`);
+                log.info("Use --force to add anyway.");
+                process.exit(1);
+            }
+        }
         const title = options.title ?? pdfMeta?.title ?? path.basename(litPath, path.extname(litPath));
         // Create literature record
         const literature = litOps.createLiterature({
@@ -249,6 +260,7 @@ export function createLiteratureCommand() {
         .command("list <knowledge-base-id>")
         .description("List literatures in a knowledge base")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action((kbId, options) => {
         const resolved = resolveKnowledgeBase(kbId);
         if (!resolved) {
@@ -258,16 +270,16 @@ export function createLiteratureCommand() {
         const litOps = getLitOps(resolved.scope);
         const literatures = litOps.listLiteratures(kbId);
         if (literatures.length === 0) {
-            if (options.json) {
-                log.plain("[]");
+            if (options.json || options.jq) {
+                outputJson([], options.jq);
             }
             else {
                 log.info("No literatures found.");
             }
             return;
         }
-        if (options.json) {
-            log.plain(JSON.stringify(literatures, null, 2));
+        if (options.json || options.jq) {
+            outputJson(literatures, options.jq);
             return;
         }
         const filesDir = getFilesDir(getBaseDir(resolved.scope));
@@ -292,6 +304,7 @@ export function createLiteratureCommand() {
         .option("-k, --keyword <keyword>", "Keyword substring")
         .option("--doi <doi>", "DOI substring")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action((kbId, options) => {
         const resolved = resolveKnowledgeBase(kbId);
         if (!resolved) {
@@ -313,16 +326,16 @@ export function createLiteratureCommand() {
             doi: options.doi,
         });
         if (results.length === 0) {
-            if (options.json) {
-                log.plain("[]");
+            if (options.json || options.jq) {
+                outputJson([], options.jq);
             }
             else {
                 log.info("No literatures found.");
             }
             return;
         }
-        if (options.json) {
-            log.plain(JSON.stringify(results, null, 2));
+        if (options.json || options.jq) {
+            outputJson(results, options.jq);
             return;
         }
         for (const l of results) {
@@ -344,6 +357,7 @@ export function createLiteratureCommand() {
         .command("show <knowledge-base-id> <id>")
         .description("Show literature details")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action((kbId, id, options) => {
         const resolved = resolveKnowledgeBase(kbId);
         if (!resolved) {
@@ -356,8 +370,8 @@ export function createLiteratureCommand() {
             log.error(`Literature not found: ${id}`);
             process.exit(1);
         }
-        if (options.json) {
-            log.plain(JSON.stringify(literature, null, 2));
+        if (options.json || options.jq) {
+            outputJson(literature, options.jq);
             return;
         }
         const filesDir = getFilesDir(getBaseDir(resolved.scope));
@@ -369,14 +383,15 @@ export function createLiteratureCommand() {
         .command("list <literature-id>")
         .description("List all notes for a literature")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action((litId, options) => {
         const literature = findLiterature(litId);
         if (!literature) {
             log.error(`Literature not found: ${litId}`);
             process.exit(1);
         }
-        if (options.json) {
-            log.plain(JSON.stringify(literature.notes, null, 2));
+        if (options.json || options.jq) {
+            outputJson(literature.notes, options.jq);
             return;
         }
         const entries = Object.entries(literature.notes);

package/dist/commands/output.js

@@ -0,0 +1,25 @@
+import { jq } from "@eurfelux/jq-js";
+import { log } from "../logger.js";
+/**
+ * Output data as JSON, optionally filtered by a jq expression.
+ * When `jqExpr` is provided, applies the jq filter and prints each result value.
+ * Otherwise prints pretty-printed JSON.
+ */
+export function outputJson(data, jqExpr) {
+    const jsonStr = JSON.stringify(data, null, 2);
+    if (jqExpr) {
+        const normalized = JSON.parse(jsonStr);
+        const results = jq(jqExpr, normalized);
+        for (const result of results) {
+            if (typeof result === "string") {
+                log.plain(result);
+            }
+            else {
+                log.plain(JSON.stringify(result, null, 2));
+            }
+        }
+    }
+    else {
+        log.plain(jsonStr);
+    }
+}

package/dist/commands/util.js

@@ -3,6 +3,7 @@ import path from "node:path";
 import { Command } from "commander";
 import { extractPdfMetadata } from "../extractor/pdf.js";
 import { log } from "../logger.js";
+import { outputJson } from "./output.js";
 export function createUtilCommand() {
     const util = new Command("util").description("Utility commands");
     util
@@ -26,6 +27,7 @@ export function createUtilCommand() {
         .command("pdf-meta <file>")
         .description("Extract metadata from a PDF file")
         .option("--json", "Output as JSON")
+        .option("--jq <expression>", "Filter JSON output with a jq expression (implies --json)")
         .action(async (file, options) => {
         const absolutePath = path.resolve(file);
         if (!existsSync(absolutePath)) {
@@ -44,8 +46,8 @@ export function createUtilCommand() {
             log.error(`Failed to parse PDF: ${err instanceof Error ? err.message : String(err)}`);
             process.exit(1);
         }
-        if (options.json) {
-            log.plain(JSON.stringify(meta, null, 2));
+        if (options.json || options.jq) {
+            outputJson(meta, options.jq);
             return;
         }
         log.header("PDF Metadata");

package/dist/db/operations/literatures.js

@@ -85,6 +85,14 @@ export function updateLiterature(db, id, input) {
     const row = db.update(literatures).set(updates).where(eq(literatures.id, id)).returning().get();
     return row ?? null;
 }
+export function findLiteratureByDoi(db, knowledgeBaseId, doi) {
+    const row = db
+        .select()
+        .from(literatures)
+        .where(and(eq(literatures.knowledgeBaseId, knowledgeBaseId), eq(literatures.doi, doi)))
+        .get();
+    return row ?? null;
+}
 export function deleteLiterature(db, id) {
     const result = db.delete(literatures).where(eq(literatures.id, id)).run();
     return result.changes > 0;

package/dist/db/project/literatures.js

@@ -21,6 +21,9 @@ export function deleteLiteraturesByKnowledgeBaseId(knowledgeBaseId) {
 export function searchLiteratures(knowledgeBaseId, filters) {
     return ops.searchLiteratures(getProjectDb(), knowledgeBaseId, filters);
 }
+export function findLiteratureByDoi(knowledgeBaseId, doi) {
+    return ops.findLiteratureByDoi(getProjectDb(), knowledgeBaseId, doi);
+}
 export function getLiteraturesByKnowledgeBaseId(knowledgeBaseId) {
     return ops.getLiteraturesByKnowledgeBaseId(getProjectDb(), knowledgeBaseId);
 }

package/dist/db/user/literatures.js

@@ -21,6 +21,9 @@ export function deleteLiteraturesByKnowledgeBaseId(knowledgeBaseId) {
 export function searchLiteratures(knowledgeBaseId, filters) {
     return ops.searchLiteratures(getUserDb(), knowledgeBaseId, filters);
 }
+export function findLiteratureByDoi(knowledgeBaseId, doi) {
+    return ops.findLiteratureByDoi(getUserDb(), knowledgeBaseId, doi);
+}
 export function getLiteraturesByKnowledgeBaseId(knowledgeBaseId) {
     return ops.getLiteraturesByKnowledgeBaseId(getUserDb(), knowledgeBaseId);
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "paper-manager",
-  "version": "0.10.4",
+  "version": "0.11.1",
   "description": "A paper management system.",
   "keywords": [],
   "homepage": "https://github.com/EurFelux/paper-manager",
@@ -21,6 +21,7 @@
   "dependencies": {
     "@ai-sdk/openai": "^3.0.37",
     "@ai-sdk/provider": "^3.0.8",
+    "@eurfelux/jq-js": "^0.3.0",
     "ai": "^6.0.105",
     "better-sqlite3": "^12.6.2",
     "chalk": "^5.6.2",