objectivist-ner 0.0.4 → 0.0.9

package/dist/index.d.ts

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+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../index.ts"],"names":[],"mappings":""}

package/dist/index.js

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+import { program } from "commander";
+import path from "path";
+import os from "os";
+import fs from "fs";
+import { getLlama, LlamaChatSession, resolveModelFile } from "node-llama-cpp";
+// === MODELS ===
+const MODELS = {
+    fast: "hf:unsloth/Qwen3.5-0.8B-GGUF:Qwen3.5-0.8B-Q8_0.gguf",
+    balanced: "hf:unsloth/Qwen3.5-2B-GGUF:Qwen3.5-2B-Q8_0.gguf",
+    best: "hf:unsloth/Qwen3.5-4B-GGUF:Qwen3.5-4B-Q8_0.gguf",
+};
+// === SYSTEM PROMPTS ===
+const SYSTEM_PROMPT = `You are a named entity recognition (NER) system. Your task is to extract entities from text.
+
+Rules:
+- "text" must be the EXACT substring from the input that refers to the entity. Do NOT paraphrase or include extra words.
+- "class" is the entity type (e.g. person, animal, location, organization).
+- "attributes" are properties of the entity found in context.
+- Return one object per distinct entity mention.
+- If no entities are found, return an empty array [].`;
+const FEW_SHOT_EXAMPLES = `Example 1:
+Input: "the cat is blue and is feeling sad"
+Output: [{"class":"animal","text":"cat","attributes":{"color":"blue","emotional_state":"sad"}}]
+
+Example 2:
+Input: "John Smith lives in New York City and works at Google"
+Output: [{"class":"person","text":"John Smith","attributes":{"location":"New York City","employer":"Google"}},{"class":"location","text":"New York City","attributes":{}},{"class":"organization","text":"Google","attributes":{}}]
+
+Example 3:
+Input: "The quick brown fox jumps over the lazy dog near the river"
+Output: [{"class":"animal","text":"fox","attributes":{"color":"brown","speed":"quick"}},{"class":"animal","text":"dog","attributes":{"temperament":"lazy"}},{"class":"location","text":"the river","attributes":{}}]
+
+Example 4:
+Input: "Researchers at MIT found that the drug Riluzole slows progression of ALS in a trial last March"
+Output: [{"class":"organization","text":"MIT","attributes":{}},{"class":"drug","text":"Riluzole","attributes":{}},{"class":"disease","text":"ALS","attributes":{}},{"class":"event","text":"trial last March","attributes":{"date":"last March"}}]`;
+// === TAXONOMY HELPERS ===
+// Taxonomy format: {"organism": ["person", {"animal": ["dog", "cat"]}], "idea": ["dream", "principle"]}
+// Arrays contain leaf nodes, objects contain nested taxonomies
+function getLeafNodes(taxonomy) {
+    const leaves = [];
+    function traverse(node) {
+        if (Array.isArray(node)) {
+            for (const item of node) {
+                if (typeof item === "string") {
+                    leaves.push(item);
+                }
+                else if (typeof item === "object" && item !== null) {
+                    traverse(item);
+                }
+            }
+        }
+        else if (typeof node === "object" && node !== null) {
+            for (const [, value] of Object.entries(node)) {
+                traverse(value);
+            }
+        }
+    }
+    traverse(taxonomy);
+    return leaves;
+}
+function getTaxonomyPath(leaf, taxonomy) {
+    function findPath(node, target, currentPath) {
+        if (Array.isArray(node)) {
+            for (const item of node) {
+                if (typeof item === "string" && item === target) {
+                    return [...currentPath, item];
+                }
+                else if (typeof item === "object" && item !== null) {
+                    const result = findPath(item, target, currentPath);
+                    if (result)
+                        return result;
+                }
+            }
+        }
+        else if (typeof node === "object" && node !== null) {
+            for (const [key, value] of Object.entries(node)) {
+                const result = findPath(value, target, [...currentPath, key]);
+                if (result)
+                    return result;
+            }
+        }
+        return null;
+    }
+    // Try each root node
+    for (const [rootKey, rootValue] of Object.entries(taxonomy)) {
+        const path = findPath(rootValue, leaf, [rootKey]);
+        if (path)
+            return path;
+    }
+    return [leaf];
+}
+function taxonomyToPrompt(taxonomy) {
+    function formatNode(node, indent) {
+        const lines = [];
+        if (Array.isArray(node)) {
+            for (const item of node) {
+                if (typeof item === "string") {
+                    lines.push(`${indent}- ${item}`);
+                }
+                else if (typeof item === "object" && item !== null) {
+                    lines.push(...formatNode(item, indent));
+                }
+            }
+        }
+        else if (typeof node === "object" && node !== null) {
+            for (const [key, value] of Object.entries(node)) {
+                lines.push(`${indent}- ${key}`);
+                lines.push(...formatNode(value, indent + "  "));
+            }
+        }
+        return lines;
+    }
+    const lines = [
+        "Use the following class hierarchy. Classify at the most specific (leaf) level:",
+    ];
+    for (const [rootKey, rootValue] of Object.entries(taxonomy)) {
+        lines.push(`- ${rootKey}`);
+        lines.push(...formatNode(rootValue, "  "));
+    }
+    return lines.join("\n");
+}
+// === CHUNKING ===
+function chunkText(text, maxChars) {
+    if (text.length <= maxChars)
+        return [text];
+    const chunks = [];
+    const sentences = text.split(/(?<=[.!?])\s+/);
+    let current = "";
+    for (const sentence of sentences) {
+        if (current.length + sentence.length > maxChars && current.length > 0) {
+            chunks.push(current.trim());
+            current = "";
+        }
+        current += (current ? " " : "") + sentence;
+    }
+    if (current.trim())
+        chunks.push(current.trim());
+    return chunks;
+}
+// === CLI ===
+program
+    .name("ner")
+    .description("Objectivist-inspired named entity recognition with grammar constraints")
+    .argument("[text]", "Text to extract entities from (omit to read from stdin)")
+    .option("-c, --classes <list>", "Comma-separated allowed entity classes")
+    .option("-a, --attributes <list>", "Comma-separated allowed attribute keys")
+    .option("--attr-values <json>", 'JSON enum map for attributes e.g. {"color":["blue","red"]}')
+    .option("--taxonomy <json>", 'Class hierarchy JSON e.g. {"organism":["animal","plant"]}')
+    .option("--relations", "Extract relations between entities")
+    .option("--relation-classes <list>", "Comma-separated allowed relation classes (e.g. employment,location,causal)")
+    .option("--resolve", "Resolve coreferences (group mentions of same entity)")
+    .option("--include-confidence", "Include confidence scores per entity")
+    .option("--detect-negation", "Detect negated/hypothetical entities")
+    .option("--schema <path>", "Load entity schema definition from a JSON file")
+    .option("--file <path>", "Read input from a file (with chunking for long docs)")
+    .option("--batch <path>", "Process JSONL file (one text per line) or directory of .txt files")
+    .option("--system-prompt <string>", "Replace the built-in system prompt entirely")
+    .option("--system-prompt-append <string>", "Append to the built-in system prompt")
+    .option("-m, --model <uri>", "Model URI or path to GGUF file")
+    .option("--fast", "Use smallest model (0.8B) -- quick, simple text only")
+    .option("--balanced", "Use mid-size model (2B) -- good accuracy/speed tradeoff")
+    .option("--best", "Use largest model (4B) -- best accuracy (default)")
+    .option("--compact", "Output compact JSON (also auto-enabled for non-TTY)")
+    .addHelpText("after", `
+Examples:
+  ner "the cat is blue"
+  ner "John works at Google" --classes person,organization
+  ner "sky is blue" --attr-values '{"color":["blue","red"]}'
+  ner --relations "Dr. Chen works at MIT"
+  ner --resolve "Dr. Chen published a paper. She won an award."
+  ner --detect-negation "The patient does not have cancer"
+  ner --schema schema.json "complex text"
+  ner --file document.txt
+  ner --batch inputs.jsonl
+  echo "the cat is blue" | ner
+`)
+    .parse();
+const opts = program.opts();
+// === VALIDATIONS ===
+const tierFlags = [opts.fast, opts.balanced, opts.best].filter(Boolean).length;
+if (tierFlags > 1) {
+    console.error("Error: --fast, --balanced, and --best are mutually exclusive.");
+    process.exit(1);
+}
+if (opts.systemPrompt && opts.systemPromptAppend) {
+    console.error("Error: --system-prompt and --system-prompt-append are mutually exclusive.");
+    process.exit(1);
+}
+// === LOAD SCHEMA FILE ===
+let schemaFile;
+if (opts.schema) {
+    try {
+        const raw = fs.readFileSync(opts.schema, "utf-8");
+        schemaFile = JSON.parse(raw);
+    }
+    catch (e) {
+        console.error(`Error: Failed to load schema file: ${e.message}`);
+        process.exit(1);
+    }
+}
+// === MERGE OPTIONS (CLI flags override schema file) ===
+const allowedClasses = opts.classes
+    ? opts.classes.split(",").map((s) => s.trim())
+    : schemaFile?.classes;
+const allowedAttrs = opts.attributes
+    ? opts.attributes.split(",").map((s) => s.trim())
+    : schemaFile?.attributes;
+let attrValuesMap;
+if (opts.attrValues) {
+    try {
+        attrValuesMap = JSON.parse(opts.attrValues);
+    }
+    catch (e) {
+        console.error(`Error: Invalid JSON for --attr-values: ${e.message}`);
+        process.exit(1);
+    }
+}
+else if (schemaFile?.attrValues) {
+    attrValuesMap = schemaFile.attrValues;
+}
+let taxonomy;
+if (opts.taxonomy) {
+    try {
+        taxonomy = JSON.parse(opts.taxonomy);
+    }
+    catch (e) {
+        console.error(`Error: Invalid JSON for --taxonomy: ${e.message}`);
+        process.exit(1);
+    }
+}
+else if (schemaFile?.taxonomy) {
+    taxonomy = schemaFile.taxonomy;
+}
+const enableRelations = opts.relations || !!schemaFile?.relations;
+const relationTypes = schemaFile?.relations || undefined;
+const relationClasses = opts.relationClasses
+    ? opts.relationClasses.split(",").map((s) => s.trim())
+    : schemaFile?.relationClasses;
+const enableResolve = !!opts.resolve;
+const enableConfidence = !!opts.includeConfidence;
+const enableNegation = !!opts.detectNegation;
+// === READ INPUT ===
+let inputTexts = [];
+if (opts.batch) {
+    const batchPath = opts.batch;
+    const stat = fs.statSync(batchPath);
+    if (stat.isDirectory()) {
+        const files = fs
+            .readdirSync(batchPath)
+            .filter((f) => f.endsWith(".txt"));
+        inputTexts = files.map((f) => fs.readFileSync(path.join(batchPath, f), "utf-8").trim());
+    }
+    else {
+        const content = fs.readFileSync(batchPath, "utf-8").trim();
+        inputTexts = content.split("\n").map((line) => {
+            try {
+                const parsed = JSON.parse(line);
+                return typeof parsed === "string" ? parsed : parsed.text || line;
+            }
+            catch {
+                return line;
+            }
+        });
+    }
+}
+else if (opts.file) {
+    const content = fs.readFileSync(opts.file, "utf-8").trim();
+    inputTexts = chunkText(content, 2000);
+}
+else {
+    let text = program.args[0];
+    if (!text) {
+        const chunks = [];
+        for await (const chunk of process.stdin) {
+            chunks.push(chunk);
+        }
+        text = Buffer.concat(chunks).toString().trim();
+    }
+    if (!text) {
+        console.error("Error: No input text provided. Pass as argument, --file, --batch, or stdin.");
+        process.exit(1);
+    }
+    inputTexts = [text];
+}
+// === RESOLVE MODEL ===
+const modelUri = opts.model
+    ? opts.model
+    : opts.fast
+        ? MODELS.fast
+        : opts.balanced
+            ? MODELS.balanced
+            : MODELS.best;
+const modelsDir = path.join(os.homedir(), ".fastner", "models");
+const modelPath = await resolveModelFile(modelUri, modelsDir);
+const llama = await getLlama();
+const model = await llama.loadModel({ modelPath });
+const context = await model.createContext();
+// === BUILD SYSTEM PROMPT ===
+function buildSystemPrompt() {
+    if (opts.systemPrompt)
+        return opts.systemPrompt;
+    let base = SYSTEM_PROMPT;
+    if (enableNegation) {
+        base += `\n- Every entity has a top-level "assertion" field: "present", "negated", or "hypothetical". "negated" means the text explicitly denies it (e.g. "does not have"). "hypothetical" means it is speculative (e.g. "might develop").`;
+    }
+    if (enableConfidence) {
+        base += `\n- Every entity has a top-level "confidence" field: "low", "medium", or "high".`;
+    }
+    if (enableResolve) {
+        base += `\n- Every entity has a top-level "entity_id" field. If multiple text spans refer to the same real-world entity (e.g. "Dr. Chen" and "she"), they share the same entity_id. Use short IDs like "e1", "e2".`;
+        base += `\n- When multiple mentions share an entity_id, exactly ONE of them must have "is_canonical": true (the most specific reference like a proper name). The others must have "is_canonical": false.`;
+    }
+    let prompt = `${base}\n\n${FEW_SHOT_EXAMPLES}`;
+    if (opts.systemPromptAppend) {
+        prompt += `\n\n${opts.systemPromptAppend}`;
+    }
+    return prompt;
+}
+// === BUILD GRAMMAR SCHEMA ===
+function buildGrammarSchema() {
+    // When using taxonomy, only allow leaf nodes as valid classes.
+    // This forces the model to classify at the most specific level.
+    const classEnum = taxonomy ? getLeafNodes(taxonomy) : allowedClasses;
+    const attributesSchema = {
+        type: "object",
+        additionalProperties: { type: "string" },
+    };
+    const properties = {
+        class: {
+            type: "string",
+            ...(classEnum && { enum: classEnum }),
+        },
+        text: { type: "string" },
+        attributes: attributesSchema,
+    };
+    const required = ["class", "text"];
+    // Grammar-enforced fields for enabled features.
+    // These are top-level entity properties (not inside attributes)
+    // so the grammar can enforce them as required on every entity.
+    if (enableNegation) {
+        properties.assertion = {
+            type: "string",
+            enum: ["present", "negated", "hypothetical"],
+        };
+        required.push("assertion");
+    }
+    if (enableConfidence) {
+        properties.confidence = {
+            type: "string",
+            enum: ["low", "medium", "high"],
+        };
+        required.push("confidence");
+    }
+    if (enableResolve) {
+        properties.entity_id = { type: "string" };
+        properties.is_canonical = { type: "boolean" };
+        required.push("entity_id");
+        required.push("is_canonical");
+    }
+    const schema = {
+        type: "array",
+        items: {
+            type: "object",
+            properties,
+            required,
+            additionalProperties: false,
+        },
+    };
+    return schema;
+}
+// === BUILD RELATIONS SCHEMA ===
+function buildRelationsSchema() {
+    const relationProperties = {
+        source: { type: "string" },
+        target: { type: "string" },
+        relation: {
+            type: "string",
+            ...(relationTypes && { enum: relationTypes }),
+        },
+    };
+    // Add class field if relationClasses is specified
+    if (relationClasses) {
+        relationProperties.class = {
+            type: "string",
+            enum: relationClasses,
+        };
+    }
+    const relSchema = {
+        type: "object",
+        properties: {
+            entities: buildGrammarSchema(),
+            relations: {
+                type: "array",
+                items: {
+                    type: "object",
+                    properties: relationProperties,
+                    required: relationClasses
+                        ? ["source", "target", "relation", "class"]
+                        : ["source", "target", "relation"],
+                    additionalProperties: false,
+                },
+            },
+        },
+        required: ["entities", "relations"],
+        additionalProperties: false,
+    };
+    return relSchema;
+}
+// === BUILD PROMPT CONSTRAINTS ===
+function buildConstraints() {
+    let constraints = "";
+    if (taxonomy) {
+        constraints += `\n${taxonomyToPrompt(taxonomy)}`;
+    }
+    else if (allowedClasses) {
+        constraints += `\nAllowed entity classes: ${allowedClasses.join(", ")}. Only use these classes.`;
+    }
+    if (attrValuesMap) {
+        const desc = Object.entries(attrValuesMap)
+            .map(([k, v]) => `${k}: ${v.join(", ")}`)
+            .join("; ");
+        constraints += `\nOnly use these attribute keys and values: ${desc}. Omit attributes that don't apply to an entity.`;
+    }
+    else if (allowedAttrs) {
+        constraints += `\nOnly use these attribute keys: ${allowedAttrs.join(", ")}. Omit attributes that don't apply to an entity.`;
+    }
+    if (enableNegation) {
+        constraints += `\nEvery entity has an "assertion" field (not in attributes). Example: [{"class":"disease","text":"diabetes","assertion":"present","attributes":{}},{"class":"disease","text":"cancer","assertion":"negated","attributes":{}}]`;
+    }
+    if (enableConfidence) {
+        constraints += `\nEvery entity has a "confidence" field (not in attributes). Example: [{"class":"person","text":"John","confidence":"high","attributes":{}}]`;
+    }
+    if (enableResolve) {
+        constraints += `\nEvery entity has "entity_id" and "is_canonical" fields. Coreferent mentions share entity_id; exactly one per group has is_canonical:true (the most specific reference). Example: [{"class":"person","text":"Dr. Chen","entity_id":"e1","is_canonical":true,"attributes":{}},{"class":"person","text":"She","entity_id":"e1","is_canonical":false,"attributes":{}}]`;
+    }
+    if (enableRelations) {
+        let relDesc = `\nAlso extract relations between entities.`;
+        if (relationClasses) {
+            relDesc += ` Each relation must have a "class" field categorizing the relation type.`;
+        }
+        relDesc += ` Return {"entities": [...], "relations": [{"source": "entity text", "target": "entity text", "relation": "relation type"${relationClasses ? ', "class": "relation class"' : ""}}]}.`;
+        constraints += relDesc;
+        if (relationTypes) {
+            constraints += ` Allowed relation types: ${relationTypes.join(", ")}.`;
+        }
+        if (relationClasses) {
+            constraints += ` Allowed relation classes: ${relationClasses.join(", ")}.`;
+        }
+    }
+    return constraints;
+}
+// === PROCESS A SINGLE TEXT ===
+async function processText(inputText, session) {
+    const constraints = buildConstraints();
+    const prompt = `Extract all named entities from the following text.${constraints}\n\nText: ${inputText}`;
+    const schema = enableRelations
+        ? buildRelationsSchema()
+        : buildGrammarSchema();
+    const grammar = await llama.createGrammarForJsonSchema(schema);
+    const res = await session.prompt(prompt, { grammar });
+    let parsed;
+    try {
+        parsed = grammar.parse(res);
+    }
+    catch {
+        try {
+            parsed = JSON.parse(res.trim());
+        }
+        catch {
+            console.error("Warning: Failed to parse model output. Raw response:", res);
+            parsed = enableRelations ? { entities: [], relations: [] } : [];
+        }
+    }
+    // If taxonomy is used, add taxonomyPath showing full hierarchy
+    if (taxonomy && !enableRelations && Array.isArray(parsed)) {
+        for (const entity of parsed) {
+            if (entity.class && typeof entity.class === "string") {
+                entity.taxonomyPath = getTaxonomyPath(entity.class, taxonomy);
+            }
+        }
+    }
+    return parsed;
+}
+// === MAIN ===
+const systemPrompt = buildSystemPrompt();
+const compact = opts.compact || !process.stdout.isTTY;
+const contextSequence = context.getSequence();
+if (inputTexts.length === 1) {
+    const session = new LlamaChatSession({
+        contextSequence,
+        systemPrompt,
+    });
+    const result = await processText(inputTexts[0], session);
+    console.log(JSON.stringify(result, null, compact ? 0 : 2));
+}
+else {
+    // Batch / chunked: process each text, collect results
+    const allResults = [];
+    for (const inputText of inputTexts) {
+        // Erase context and create fresh session for each input
+        await contextSequence.eraseContextTokenRanges([
+            { start: 0, end: contextSequence.nextTokenIndex },
+        ]);
+        const session = new LlamaChatSession({
+            contextSequence,
+            systemPrompt,
+        });
+        const result = await processText(inputText, session);
+        allResults.push(result);
+    }
+    if (opts.file) {
+        // Merge chunked results into one
+        if (enableRelations) {
+            const merged = {
+                entities: allResults.flatMap((r) => r.entities || []),
+                relations: allResults.flatMap((r) => r.relations || []),
+            };
+            console.log(JSON.stringify(merged, null, compact ? 0 : 2));
+        }
+        else {
+            const merged = allResults.flat();
+            console.log(JSON.stringify(merged, null, compact ? 0 : 2));
+        }
+    }
+    else {
+        // Batch: output one result per line (JSONL)
+        for (const result of allResults) {
+            console.log(JSON.stringify(result));
+        }
+    }
+}
+// === CLEANUP ===
+// Bun segfaults if process.exit() triggers synchronous native addon unloading.
+// Setting exitCode lets the event loop drain naturally, avoiding the crash.
+process.exitCode = 0;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/package.json

@@ -1,21 +1,35 @@
 {
   "name": "objectivist-ner",
-  "version": "0.0.4",
+  "version": "0.0.9",
   "description": "Objectivist-inspired Named Entity Recognition with grammar-constrained LLM output",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
   "bin": {
-    "ner": "index.ts"
+    "ner": "dist/index.js"
   },
-  "module": "index.ts",
   "type": "module",
   "license": "MIT",
   "author": "Richard Anaya",
   "repository": "git@github.com:richardanaya/objectivist-ner.git",
-  "devDependencies": {
-    "@types/bun": "latest",
-    "prettier": "^3.8.1"
+  "files": [
+    "dist/",
+    "LICENSE",
+    "README.md"
+  ],
+  "scripts": {
+    "dev": "tsx index.ts",
+    "build": "tsc",
+    "prepublishOnly": "npm run build",
+    "postinstall": "node-llama-cpp download || true"
+  },
+  "engines": {
+    "node": ">=18"
   },
-  "peerDependencies": {
-    "typescript": "^5"
+  "devDependencies": {
+    "@types/node": "^20.0.0",
+    "prettier": "^3.8.1",
+    "tsx": "^4.0.0",
+    "typescript": "^5.0.0"
   },
   "dependencies": {
     "commander": "^14.0.3",

package/index.ts

@@ -1,635 +0,0 @@
-#!/usr/bin/env bun
-import { program } from "commander";
-import path from "path";
-import os from "os";
-import fs from "fs";
-import { getLlama, LlamaChatSession, resolveModelFile } from "node-llama-cpp";
-
-// === MODELS ===
-const MODELS = {
-  fast: "hf:unsloth/Qwen3.5-0.8B-GGUF:Qwen3.5-0.8B-Q8_0.gguf",
-  balanced: "hf:unsloth/Qwen3.5-2B-GGUF:Qwen3.5-2B-Q8_0.gguf",
-  best: "hf:unsloth/Qwen3.5-4B-GGUF:Qwen3.5-4B-Q8_0.gguf",
-} as const;
-
-// === SYSTEM PROMPTS ===
-const SYSTEM_PROMPT = `You are a named entity recognition (NER) system. Your task is to extract entities from text.
-
-Rules:
-- "text" must be the EXACT substring from the input that refers to the entity. Do NOT paraphrase or include extra words.
-- "class" is the entity type (e.g. person, animal, location, organization).
-- "attributes" are properties of the entity found in context.
-- Return one object per distinct entity mention.
-- If no entities are found, return an empty array [].`;
-
-const FEW_SHOT_EXAMPLES = `Example 1:
-Input: "the cat is blue and is feeling sad"
-Output: [{"class":"animal","text":"cat","attributes":{"color":"blue","emotional_state":"sad"}}]
-
-Example 2:
-Input: "John Smith lives in New York City and works at Google"
-Output: [{"class":"person","text":"John Smith","attributes":{"location":"New York City","employer":"Google"}},{"class":"location","text":"New York City","attributes":{}},{"class":"organization","text":"Google","attributes":{}}]
-
-Example 3:
-Input: "The quick brown fox jumps over the lazy dog near the river"
-Output: [{"class":"animal","text":"fox","attributes":{"color":"brown","speed":"quick"}},{"class":"animal","text":"dog","attributes":{"temperament":"lazy"}},{"class":"location","text":"the river","attributes":{}}]
-
-Example 4:
-Input: "Researchers at MIT found that the drug Riluzole slows progression of ALS in a trial last March"
-Output: [{"class":"organization","text":"MIT","attributes":{}},{"class":"drug","text":"Riluzole","attributes":{}},{"class":"disease","text":"ALS","attributes":{}},{"class":"event","text":"trial last March","attributes":{"date":"last March"}}]`;
-
-// === SCHEMA FILE TYPES ===
-interface SchemaFile {
-  taxonomy?: Record<string, string[]>;
-  classes?: string[];
-  attributes?: string[];
-  attrValues?: Record<string, string[]>;
-  relations?: string[];
-  relationClasses?: string[];
-}
-
-// === TAXONOMY HELPERS ===
-// Taxonomy format: {"organism": ["person", {"animal": ["dog", "cat"]}], "idea": ["dream", "principle"]}
-// Arrays contain leaf nodes, objects contain nested taxonomies
-
-function getLeafNodes(taxonomy: Record<string, any>): string[] {
-  const leaves: string[] = [];
-
-  function traverse(node: any) {
-    if (Array.isArray(node)) {
-      for (const item of node) {
-        if (typeof item === "string") {
-          leaves.push(item);
-        } else if (typeof item === "object" && item !== null) {
-          traverse(item);
-        }
-      }
-    } else if (typeof node === "object" && node !== null) {
-      for (const [, value] of Object.entries(node)) {
-        traverse(value);
-      }
-    }
-  }
-
-  traverse(taxonomy);
-  return leaves;
-}
-
-function getTaxonomyPath(
-  leaf: string,
-  taxonomy: Record<string, any>,
-): string[] {
-  function findPath(
-    node: any,
-    target: string,
-    currentPath: string[],
-  ): string[] | null {
-    if (Array.isArray(node)) {
-      for (const item of node) {
-        if (typeof item === "string" && item === target) {
-          return [...currentPath, item];
-        } else if (typeof item === "object" && item !== null) {
-          const result = findPath(item, target, currentPath);
-          if (result) return result;
-        }
-      }
-    } else if (typeof node === "object" && node !== null) {
-      for (const [key, value] of Object.entries(node)) {
-        const result = findPath(value, target, [...currentPath, key]);
-        if (result) return result;
-      }
-    }
-    return null;
-  }
-
-  // Try each root node
-  for (const [rootKey, rootValue] of Object.entries(taxonomy)) {
-    const path = findPath(rootValue, leaf, [rootKey]);
-    if (path) return path;
-  }
-
-  return [leaf];
-}
-
-function taxonomyToPrompt(taxonomy: Record<string, any>): string {
-  function formatNode(node: any, indent: string): string[] {
-    const lines: string[] = [];
-
-    if (Array.isArray(node)) {
-      for (const item of node) {
-        if (typeof item === "string") {
-          lines.push(`${indent}- ${item}`);
-        } else if (typeof item === "object" && item !== null) {
-          lines.push(...formatNode(item, indent));
-        }
-      }
-    } else if (typeof node === "object" && node !== null) {
-      for (const [key, value] of Object.entries(node)) {
-        lines.push(`${indent}- ${key}`);
-        lines.push(...formatNode(value, indent + "  "));
-      }
-    }
-
-    return lines;
-  }
-
-  const lines: string[] = [
-    "Use the following class hierarchy. Classify at the most specific (leaf) level:",
-  ];
-
-  for (const [rootKey, rootValue] of Object.entries(taxonomy)) {
-    lines.push(`- ${rootKey}`);
-    lines.push(...formatNode(rootValue, "  "));
-  }
-
-  return lines.join("\n");
-}
-
-// === CHUNKING ===
-function chunkText(text: string, maxChars: number): string[] {
-  if (text.length <= maxChars) return [text];
-  const chunks: string[] = [];
-  const sentences = text.split(/(?<=[.!?])\s+/);
-  let current = "";
-  for (const sentence of sentences) {
-    if (current.length + sentence.length > maxChars && current.length > 0) {
-      chunks.push(current.trim());
-      current = "";
-    }
-    current += (current ? " " : "") + sentence;
-  }
-  if (current.trim()) chunks.push(current.trim());
-  return chunks;
-}
-
-// === CLI ===
-program
-  .name("ner")
-  .description(
-    "Objectivist-inspired named entity recognition with grammar constraints",
-  )
-  .argument("[text]", "Text to extract entities from (omit to read from stdin)")
-  .option("-c, --classes <list>", "Comma-separated allowed entity classes")
-  .option("-a, --attributes <list>", "Comma-separated allowed attribute keys")
-  .option(
-    "--attr-values <json>",
-    'JSON enum map for attributes e.g. {"color":["blue","red"]}',
-  )
-  .option(
-    "--taxonomy <json>",
-    'Class hierarchy JSON e.g. {"organism":["animal","plant"]}',
-  )
-  .option("--relations", "Extract relations between entities")
-  .option(
-    "--relation-classes <list>",
-    "Comma-separated allowed relation classes (e.g. employment,location,causal)",
-  )
-  .option("--resolve", "Resolve coreferences (group mentions of same entity)")
-  .option("--include-confidence", "Include confidence scores per entity")
-  .option("--detect-negation", "Detect negated/hypothetical entities")
-  .option("--schema <path>", "Load entity schema definition from a JSON file")
-  .option(
-    "--file <path>",
-    "Read input from a file (with chunking for long docs)",
-  )
-  .option(
-    "--batch <path>",
-    "Process JSONL file (one text per line) or directory of .txt files",
-  )
-  .option(
-    "--system-prompt <string>",
-    "Replace the built-in system prompt entirely",
-  )
-  .option(
-    "--system-prompt-append <string>",
-    "Append to the built-in system prompt",
-  )
-  .option("-m, --model <uri>", "Model URI or path to GGUF file")
-  .option("--fast", "Use smallest model (0.8B) -- quick, simple text only")
-  .option(
-    "--balanced",
-    "Use mid-size model (2B) -- good accuracy/speed tradeoff",
-  )
-  .option("--best", "Use largest model (4B) -- best accuracy (default)")
-  .option("--compact", "Output compact JSON (also auto-enabled for non-TTY)")
-  .addHelpText(
-    "after",
-    `
-Examples:
-  ner "the cat is blue"
-  ner "John works at Google" --classes person,organization
-  ner "sky is blue" --attr-values '{"color":["blue","red"]}'
-  ner --relations "Dr. Chen works at MIT"
-  ner --resolve "Dr. Chen published a paper. She won an award."
-  ner --detect-negation "The patient does not have cancer"
-  ner --schema schema.json "complex text"
-  ner --file document.txt
-  ner --batch inputs.jsonl
-  echo "the cat is blue" | ner
-`,
-  )
-  .parse();
-
-const opts = program.opts();
-
-// === VALIDATIONS ===
-const tierFlags = [opts.fast, opts.balanced, opts.best].filter(Boolean).length;
-if (tierFlags > 1) {
-  console.error(
-    "Error: --fast, --balanced, and --best are mutually exclusive.",
-  );
-  process.exit(1);
-}
-
-if (opts.systemPrompt && opts.systemPromptAppend) {
-  console.error(
-    "Error: --system-prompt and --system-prompt-append are mutually exclusive.",
-  );
-  process.exit(1);
-}
-
-// === LOAD SCHEMA FILE ===
-let schemaFile: SchemaFile | undefined;
-if (opts.schema) {
-  try {
-    const raw = fs.readFileSync(opts.schema, "utf-8");
-    schemaFile = JSON.parse(raw);
-  } catch (e) {
-    console.error(`Error: Failed to load schema file: ${(e as Error).message}`);
-    process.exit(1);
-  }
-}
-
-// === MERGE OPTIONS (CLI flags override schema file) ===
-const allowedClasses: string[] | undefined = opts.classes
-  ? opts.classes.split(",").map((s: string) => s.trim())
-  : schemaFile?.classes;
-
-const allowedAttrs: string[] | undefined = opts.attributes
-  ? opts.attributes.split(",").map((s: string) => s.trim())
-  : schemaFile?.attributes;
-
-let attrValuesMap: Record<string, string[]> | undefined;
-if (opts.attrValues) {
-  try {
-    attrValuesMap = JSON.parse(opts.attrValues);
-  } catch (e) {
-    console.error(
-      `Error: Invalid JSON for --attr-values: ${(e as Error).message}`,
-    );
-    process.exit(1);
-  }
-} else if (schemaFile?.attrValues) {
-  attrValuesMap = schemaFile.attrValues;
-}
-
-let taxonomy: Record<string, string[]> | undefined;
-if (opts.taxonomy) {
-  try {
-    taxonomy = JSON.parse(opts.taxonomy);
-  } catch (e) {
-    console.error(
-      `Error: Invalid JSON for --taxonomy: ${(e as Error).message}`,
-    );
-    process.exit(1);
-  }
-} else if (schemaFile?.taxonomy) {
-  taxonomy = schemaFile.taxonomy;
-}
-
-const enableRelations = opts.relations || !!schemaFile?.relations;
-const relationTypes: string[] | undefined = schemaFile?.relations || undefined;
-const relationClasses: string[] | undefined = opts.relationClasses
-  ? opts.relationClasses.split(",").map((s: string) => s.trim())
-  : schemaFile?.relationClasses;
-const enableResolve = !!opts.resolve;
-const enableConfidence = !!opts.includeConfidence;
-const enableNegation = !!opts.detectNegation;
-
-// === READ INPUT ===
-let inputTexts: string[] = [];
-
-if (opts.batch) {
-  const batchPath = opts.batch as string;
-  const stat = fs.statSync(batchPath);
-  if (stat.isDirectory()) {
-    const files = fs
-      .readdirSync(batchPath)
-      .filter((f: string) => f.endsWith(".txt"));
-    inputTexts = files.map((f: string) =>
-      fs.readFileSync(path.join(batchPath, f), "utf-8").trim(),
-    );
-  } else {
-    const content = fs.readFileSync(batchPath, "utf-8").trim();
-    inputTexts = content.split("\n").map((line: string) => {
-      try {
-        const parsed = JSON.parse(line);
-        return typeof parsed === "string" ? parsed : parsed.text || line;
-      } catch {
-        return line;
-      }
-    });
-  }
-} else if (opts.file) {
-  const content = fs.readFileSync(opts.file, "utf-8").trim();
-  inputTexts = chunkText(content, 2000);
-} else {
-  let text = program.args[0];
-  if (!text) {
-    const chunks: Buffer[] = [];
-    for await (const chunk of process.stdin) {
-      chunks.push(chunk as Buffer);
-    }
-    text = Buffer.concat(chunks).toString().trim();
-  }
-  if (!text) {
-    console.error(
-      "Error: No input text provided. Pass as argument, --file, --batch, or stdin.",
-    );
-    process.exit(1);
-  }
-  inputTexts = [text];
-}
-
-// === RESOLVE MODEL ===
-const modelUri = opts.model
-  ? opts.model
-  : opts.fast
-    ? MODELS.fast
-    : opts.balanced
-      ? MODELS.balanced
-      : MODELS.best;
-
-const modelsDir = path.join(os.homedir(), ".fastner", "models");
-const modelPath = await resolveModelFile(modelUri, modelsDir);
-
-const llama = await getLlama();
-const model = await llama.loadModel({ modelPath });
-const context = await model.createContext();
-
-// === BUILD SYSTEM PROMPT ===
-function buildSystemPrompt(): string {
-  if (opts.systemPrompt) return opts.systemPrompt;
-
-  let base = SYSTEM_PROMPT;
-
-  if (enableNegation) {
-    base += `\n- Every entity has a top-level "assertion" field: "present", "negated", or "hypothetical". "negated" means the text explicitly denies it (e.g. "does not have"). "hypothetical" means it is speculative (e.g. "might develop").`;
-  }
-  if (enableConfidence) {
-    base += `\n- Every entity has a top-level "confidence" field: "low", "medium", or "high".`;
-  }
-  if (enableResolve) {
-    base += `\n- Every entity has a top-level "entity_id" field. If multiple text spans refer to the same real-world entity (e.g. "Dr. Chen" and "she"), they share the same entity_id. Use short IDs like "e1", "e2".`;
-    base += `\n- When multiple mentions share an entity_id, exactly ONE of them must have "is_canonical": true (the most specific reference like a proper name). The others must have "is_canonical": false.`;
-  }
-
-  let prompt = `${base}\n\n${FEW_SHOT_EXAMPLES}`;
-
-  if (opts.systemPromptAppend) {
-    prompt += `\n\n${opts.systemPromptAppend}`;
-  }
-
-  return prompt;
-}
-
-// === BUILD GRAMMAR SCHEMA ===
-function buildGrammarSchema() {
-  // When using taxonomy, only allow leaf nodes as valid classes.
-  // This forces the model to classify at the most specific level.
-  const classEnum = taxonomy ? getLeafNodes(taxonomy) : allowedClasses;
-
-  const attributesSchema: any = {
-    type: "object",
-    additionalProperties: { type: "string" },
-  };
-
-  const properties: any = {
-    class: {
-      type: "string",
-      ...(classEnum && { enum: classEnum }),
-    },
-    text: { type: "string" },
-    attributes: attributesSchema,
-  };
-  const required: string[] = ["class", "text"];
-
-  // Grammar-enforced fields for enabled features.
-  // These are top-level entity properties (not inside attributes)
-  // so the grammar can enforce them as required on every entity.
-  if (enableNegation) {
-    properties.assertion = {
-      type: "string",
-      enum: ["present", "negated", "hypothetical"],
-    };
-    required.push("assertion");
-  }
-  if (enableConfidence) {
-    properties.confidence = {
-      type: "string",
-      enum: ["low", "medium", "high"],
-    };
-    required.push("confidence");
-  }
-  if (enableResolve) {
-    properties.entity_id = { type: "string" };
-    properties.is_canonical = { type: "boolean" };
-    required.push("entity_id");
-    required.push("is_canonical");
-  }
-
-  const schema: any = {
-    type: "array",
-    items: {
-      type: "object",
-      properties,
-      required,
-      additionalProperties: false,
-    },
-  };
-
-  return schema;
-}
-
-// === BUILD RELATIONS SCHEMA ===
-function buildRelationsSchema() {
-  const relationProperties: any = {
-    source: { type: "string" },
-    target: { type: "string" },
-    relation: {
-      type: "string",
-      ...(relationTypes && { enum: relationTypes }),
-    },
-  };
-
-  // Add class field if relationClasses is specified
-  if (relationClasses) {
-    relationProperties.class = {
-      type: "string",
-      enum: relationClasses,
-    };
-  }
-
-  const relSchema: any = {
-    type: "object",
-    properties: {
-      entities: buildGrammarSchema(),
-      relations: {
-        type: "array",
-        items: {
-          type: "object",
-          properties: relationProperties,
-          required: relationClasses
-            ? ["source", "target", "relation", "class"]
-            : ["source", "target", "relation"],
-          additionalProperties: false,
-        },
-      },
-    },
-    required: ["entities", "relations"],
-    additionalProperties: false,
-  };
-  return relSchema;
-}
-
-// === BUILD PROMPT CONSTRAINTS ===
-function buildConstraints(): string {
-  let constraints = "";
-
-  if (taxonomy) {
-    constraints += `\n${taxonomyToPrompt(taxonomy)}`;
-  } else if (allowedClasses) {
-    constraints += `\nAllowed entity classes: ${allowedClasses.join(", ")}. Only use these classes.`;
-  }
-
-  if (attrValuesMap) {
-    const desc = Object.entries(attrValuesMap)
-      .map(([k, v]) => `${k}: ${v.join(", ")}`)
-      .join("; ");
-    constraints += `\nOnly use these attribute keys and values: ${desc}. Omit attributes that don't apply to an entity.`;
-  } else if (allowedAttrs) {
-    constraints += `\nOnly use these attribute keys: ${allowedAttrs.join(", ")}. Omit attributes that don't apply to an entity.`;
-  }
-
-  if (enableNegation) {
-    constraints += `\nEvery entity has an "assertion" field (not in attributes). Example: [{"class":"disease","text":"diabetes","assertion":"present","attributes":{}},{"class":"disease","text":"cancer","assertion":"negated","attributes":{}}]`;
-  }
-  if (enableConfidence) {
-    constraints += `\nEvery entity has a "confidence" field (not in attributes). Example: [{"class":"person","text":"John","confidence":"high","attributes":{}}]`;
-  }
-  if (enableResolve) {
-    constraints += `\nEvery entity has "entity_id" and "is_canonical" fields. Coreferent mentions share entity_id; exactly one per group has is_canonical:true (the most specific reference). Example: [{"class":"person","text":"Dr. Chen","entity_id":"e1","is_canonical":true,"attributes":{}},{"class":"person","text":"She","entity_id":"e1","is_canonical":false,"attributes":{}}]`;
-  }
-  if (enableRelations) {
-    let relDesc = `\nAlso extract relations between entities.`;
-    if (relationClasses) {
-      relDesc += ` Each relation must have a "class" field categorizing the relation type.`;
-    }
-    relDesc += ` Return {"entities": [...], "relations": [{"source": "entity text", "target": "entity text", "relation": "relation type"${relationClasses ? ', "class": "relation class"' : ""}}]}.`;
-    constraints += relDesc;
-    if (relationTypes) {
-      constraints += ` Allowed relation types: ${relationTypes.join(", ")}.`;
-    }
-    if (relationClasses) {
-      constraints += ` Allowed relation classes: ${relationClasses.join(", ")}.`;
-    }
-  }
-
-  return constraints;
-}
-
-// === PROCESS A SINGLE TEXT ===
-async function processText(
-  inputText: string,
-  session: LlamaChatSession,
-): Promise<any> {
-  const constraints = buildConstraints();
-  const prompt = `Extract all named entities from the following text.${constraints}\n\nText: ${inputText}`;
-
-  const schema = enableRelations
-    ? buildRelationsSchema()
-    : buildGrammarSchema();
-  const grammar = await llama.createGrammarForJsonSchema(schema);
-
-  const res = await session.prompt(prompt, { grammar });
-
-  let parsed: any;
-  try {
-    parsed = grammar.parse(res);
-  } catch {
-    try {
-      parsed = JSON.parse(res.trim());
-    } catch {
-      console.error(
-        "Warning: Failed to parse model output. Raw response:",
-        res,
-      );
-      parsed = enableRelations ? { entities: [], relations: [] } : [];
-    }
-  }
-
-  // If taxonomy is used, add taxonomyPath showing full hierarchy
-  if (taxonomy && !enableRelations && Array.isArray(parsed)) {
-    for (const entity of parsed) {
-      if (entity.class && typeof entity.class === "string") {
-        entity.taxonomyPath = getTaxonomyPath(entity.class, taxonomy);
-      }
-    }
-  }
-
-  return parsed;
-}
-
-// === MAIN ===
-const systemPrompt = buildSystemPrompt();
-const compact = opts.compact || !process.stdout.isTTY;
-
-const contextSequence = context.getSequence();
-
-if (inputTexts.length === 1) {
-  const session = new LlamaChatSession({
-    contextSequence,
-    systemPrompt,
-  });
-  const result = await processText(inputTexts[0]!, session);
-  console.log(JSON.stringify(result, null, compact ? 0 : 2));
-} else {
-  // Batch / chunked: process each text, collect results
-  const allResults: any[] = [];
-  for (const inputText of inputTexts) {
-    // Erase context and create fresh session for each input
-    await contextSequence.eraseContextTokenRanges([
-      { start: 0, end: contextSequence.nextTokenIndex },
-    ]);
-    const session = new LlamaChatSession({
-      contextSequence,
-      systemPrompt,
-    });
-    const result = await processText(inputText, session);
-    allResults.push(result);
-  }
-
-  if (opts.file) {
-    // Merge chunked results into one
-    if (enableRelations) {
-      const merged = {
-        entities: allResults.flatMap((r) => r.entities || []),
-        relations: allResults.flatMap((r) => r.relations || []),
-      };
-      console.log(JSON.stringify(merged, null, compact ? 0 : 2));
-    } else {
-      const merged = allResults.flat();
-      console.log(JSON.stringify(merged, null, compact ? 0 : 2));
-    }
-  } else {
-    // Batch: output one result per line (JSONL)
-    for (const result of allResults) {
-      console.log(JSON.stringify(result));
-    }
-  }
-}
-
-// === CLEANUP ===
-// Bun segfaults if process.exit() triggers synchronous native addon unloading.
-// Setting exitCode lets the event loop drain naturally, avoiding the crash.
-process.exitCode = 0;