opentology 0.2.3 → 0.2.4

package/dist/commands/context.js

@@ -11,6 +11,7 @@ import { generateContextSection, updateClaudeMd } from '../templates/claude-md-c
 import { generateHookScript } from '../templates/session-start-hook.js';
 import { generatePreEditHookScript } from '../templates/pre-edit-hook.js';
 import { generateSlashCommands } from '../templates/slash-commands.js';
+import { normalizeModuleUri } from '../lib/module-uri.js';
 function ask(question) {
     const rl = createInterface({ input: process.stdin, output: process.stdout });
     return new Promise((resolve) => {
@@ -454,7 +455,7 @@ export function registerContext(program) {
         }
         const contextUri = graphs['context'];
         const OTX = 'https://opentology.dev/vocab#';
-        const moduleUriStr = `urn:module:${opts.file}`;
+        const moduleUriStr = normalizeModuleUri(opts.file);
         try {
             const adapter = await createReadyAdapter(config);
             // Dependents (reverse deps)

package/dist/index.js

@@ -20,7 +20,7 @@ import { registerDoctor } from './commands/doctor.js';
 const program = new Command();
 program
     .name('opentology')
-    .version('0.2.2')
+    .version('0.2.4')
     .description('CLI-managed RDF/SPARQL infrastructure — Supabase for RDF');
 registerInit(program);
 registerValidate(program);

package/dist/lib/codebase-scanner.js

@@ -2,6 +2,7 @@ import { readFile, readdir } from 'node:fs/promises';
 import { join, relative } from 'node:path';
 import { execFile } from 'node:child_process';
 import { promisify } from 'node:util';
+import { stripSourceExtension } from './module-uri.js';
 const execFileAsync = promisify(execFile);
 const DEFAULT_MAX_BYTES = 15360;
 const HARDCODED_EXCLUDES = new Set(['.git', 'node_modules', 'dist', 'build', '.opentology', '.claude', '.omc']);
@@ -212,7 +213,7 @@ export async function extractDependencyGraph(rootDir, gitFiles) {
     const moduleSet = new Set();
     const edges = [];
     for (const filePath of sourceFiles) {
-        const moduleName = filePath.replace(/\.[tj]sx?$/, '');
+        const moduleName = stripSourceExtension(filePath);
         moduleSet.add(moduleName);
         let content;
         try {

package/dist/lib/deep-scan-triples.d.ts

@@ -5,11 +5,11 @@
 import type { DeepScanResult } from './deep-scanner.js';
 export declare function generateSymbolTriples(result: DeepScanResult): string[];
 export declare function batchTriples(triples: string[], batchSize?: number): string[][];
-export interface StoreAdapter {
-    sparqlUpdate(query: string): Promise<void>;
-}
+import type { StoreAdapter as FullStoreAdapter } from './store-adapter.js';
+type StoreAdapter = Pick<FullStoreAdapter, 'sparqlUpdate'>;
 export declare function deleteExistingSymbols(adapter: StoreAdapter, graphUri: string, modulePaths: string[]): Promise<void>;
 export declare function pushSymbolTriples(adapter: StoreAdapter, graphUri: string, result: DeepScanResult): Promise<{
     triplesInserted: number;
     batchCount: number;
 }>;
+export {};

package/dist/lib/deep-scan-triples.js

@@ -75,8 +75,6 @@ export function generateSymbolTriples(result) {
         }
     }
     for (const call of result.methodCalls) {
-        const callerParts = call.caller.split('.');
-        const calleeParts = call.callee.split('.');
         // Method calls reference by class.method pattern — generate a simple triple
         triples.push(`<urn:call:${encodeSegment(call.caller)}> <${OTX}calls> <urn:call:${encodeSegment(call.callee)}> .`);
         // Store caller/callee names for queryability

package/dist/lib/module-uri.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Shared module URI normalization — single source of truth for
+ * converting file paths to urn:module: URIs.
+ */
+export declare function stripSourceExtension(filePath: string): string;
+export declare function normalizeModuleUri(filePath: string): string;

package/dist/lib/module-uri.js

@@ -0,0 +1,11 @@
+/**
+ * Shared module URI normalization — single source of truth for
+ * converting file paths to urn:module: URIs.
+ */
+const SOURCE_EXT_RE = /\.[tj]sx?$/;
+export function stripSourceExtension(filePath) {
+    return filePath.replace(SOURCE_EXT_RE, '');
+}
+export function normalizeModuleUri(filePath) {
+    return `urn:module:${stripSourceExtension(filePath)}`;
+}

package/dist/lib/reasoner.d.ts

@@ -1,19 +1,8 @@
 import type { StoreAdapter } from './store-adapter.js';
-interface Triple {
-    s: string;
-    p: string;
-    o: string;
-    isLiteral: boolean;
-}
 export interface InferenceResult {
     assertedCount: number;
     inferredCount: number;
     rules: Record<string, number>;
 }
-export declare function computeInferences(triples: Triple[]): {
-    inferred: Triple[];
-    rules: Record<string, number>;
-};
 export declare function clearInferences(adapter: StoreAdapter, graphUri: string): Promise<void>;
 export declare function materializeInferences(adapter: StoreAdapter, graphUri: string): Promise<InferenceResult>;
-export {};

package/dist/lib/reasoner.js

@@ -68,7 +68,7 @@ function transitiveClosure(pairs) {
     return result;
 }
 // ── Pure inference engine ──────────────────────────────────────────────
-export function computeInferences(triples) {
+function computeInferences(triples) {
     const assertedSet = new Set(triples.map(tripleKey));
     const inferredMap = new Map(); // tripleKey → rule name
     const rules = {};

package/dist/lib/shacl.d.ts

@@ -1,10 +1,10 @@
-export interface ShaclViolation {
+interface ShaclViolation {
     focusNode: string;
     path: string | null;
     message: string;
     severity: string;
 }
-export interface ShaclReport {
+interface ShaclReport {
     conforms: boolean;
     violations: ShaclViolation[];
 }
@@ -20,3 +20,4 @@ export declare function hasShapes(shapesDir?: string): boolean;
  * Validate a Turtle data string against the given SHACL shape files.
  */
 export declare function validateWithShacl(dataTurtle: string, shapePaths: string[]): Promise<ShaclReport>;
+export {};

package/dist/lib/sparql-utils.d.ts

@@ -20,9 +20,4 @@ export declare function hasGraphScope(sparql: string): boolean;
  * Returns null if the outermost `{ ... }` block cannot be located safely.
  */
 export declare function autoScopeQuery(sparql: string, graphUri: string): string | null;
-/**
- * Auto-scope a SPARQL query with UNION over asserted + inference graphs.
- * Returns null if brace matching fails.
- */
-export declare function autoScopeQueryWithInference(sparql: string, graphUri: string, inferenceGraphUri: string): string | null;
 export declare function getInferenceGraphUri(graphUri: string): string;

package/dist/lib/sparql-utils.js

@@ -175,42 +175,6 @@ export function autoScopeQuery(sparql, graphUri) {
     const after = sparql.slice(braceEnd); // from `}` onwards
     return `${before} GRAPH <${graphUri}> {${inner}} ${after}`;
 }
-/**
- * Auto-scope a SPARQL query with UNION over asserted + inference graphs.
- * Returns null if brace matching fails.
- */
-export function autoScopeQueryWithInference(sparql, graphUri, inferenceGraphUri) {
-    const whereMatch = sparql.match(/\bWHERE\s*\{/i);
-    let braceStart;
-    if (whereMatch && whereMatch.index !== undefined) {
-        braceStart = whereMatch.index + whereMatch[0].length - 1;
-    }
-    else {
-        const firstBrace = sparql.indexOf('{');
-        if (firstBrace === -1)
-            return null;
-        braceStart = firstBrace;
-    }
-    let depth = 0;
-    let braceEnd = -1;
-    for (let i = braceStart; i < sparql.length; i++) {
-        if (sparql[i] === '{')
-            depth++;
-        else if (sparql[i] === '}') {
-            depth--;
-            if (depth === 0) {
-                braceEnd = i;
-                break;
-            }
-        }
-    }
-    if (braceEnd === -1)
-        return null;
-    const before = sparql.slice(0, braceStart + 1);
-    const inner = sparql.slice(braceStart + 1, braceEnd);
-    const after = sparql.slice(braceEnd);
-    return `${before} GRAPH ?__g {${inner}} FILTER(?__g = <${graphUri}> || ?__g = <${inferenceGraphUri}>) ${after}`;
-}
 // ── Inference graph URI ───────────────────────────────────────────────
 export function getInferenceGraphUri(graphUri) {
     return `${graphUri}/inferred`;

package/dist/lib/store-factory.d.ts

@@ -1,6 +1,5 @@
 import type { StoreAdapter } from './store-adapter.js';
 import type { OpenTologyConfig } from './config.js';
-export declare function createAdapter(config: OpenTologyConfig): StoreAdapter;
 /**
  * Reset the cached embedded adapter. Useful for tests or after config-level
  * changes that invalidate the entire store (e.g. project re-init).

package/dist/lib/store-factory.js

@@ -7,12 +7,6 @@ import { materializeInferences } from './reasoner.js';
 // Singleton cache for embedded mode — keeps data alive across MCP tool calls.
 let cachedAdapter = null;
 let loadedFileKeys = new Set();
-export function createAdapter(config) {
-    if (config.mode === 'embedded') {
-        return new EmbeddedAdapter();
-    }
-    return new HttpAdapter(config.endpoint ?? 'http://localhost:7878');
-}
 /**
  * Reset the cached embedded adapter. Useful for tests or after config-level
  * changes that invalidate the entire store (e.g. project re-init).

package/dist/mcp/server.js

@@ -5,6 +5,7 @@ import { loadConfig, saveConfig, configExists, resolveGraphUri } from '../lib/co
 import { deepScan } from '../lib/deep-scanner.js';
 import { pushSymbolTriples } from '../lib/deep-scan-triples.js';
 import { createReadyAdapter } from '../lib/store-factory.js';
+import { normalizeModuleUri } from '../lib/module-uri.js';
 import { hasGraphScope, autoScopeQuery, getInferenceGraphUri } from '../lib/sparql-utils.js';
 import { validateTurtle } from '../lib/validator.js';
 import { discoverShapes, validateWithShacl, hasShapes } from '../lib/shacl.js';
@@ -627,7 +628,7 @@ async function handleContextImpact(args) {
     const contextUri = `${config.graphUri}/context`;
     const adapter = await createReadyAdapter(config);
     const OTX = 'https://opentology.dev/vocab#';
-    const moduleUriStr = `urn:module:${filePath}`;
+    const moduleUriStr = normalizeModuleUri(filePath);
     // 1. Modules that depend on this file (dependents / reverse deps)
     const dependentsQuery = `
     SELECT ?dependent WHERE {

package/dist/templates/claude-md-context.d.ts

@@ -1,4 +1,2 @@
-export declare const MARKER_BEGIN = "<!-- OPENTOLOGY:CONTEXT:BEGIN -->";
-export declare const MARKER_END = "<!-- OPENTOLOGY:CONTEXT:END -->";
 export declare function generateContextSection(projectId: string, graphUri: string): string;
 export declare function updateClaudeMd(filePath: string, section: string): void;

package/dist/templates/claude-md-context.js

@@ -1,6 +1,6 @@
 import { readFileSync, writeFileSync, existsSync } from 'node:fs';
-export const MARKER_BEGIN = '<!-- OPENTOLOGY:CONTEXT:BEGIN -->';
-export const MARKER_END = '<!-- OPENTOLOGY:CONTEXT:END -->';
+const MARKER_BEGIN = '<!-- OPENTOLOGY:CONTEXT:BEGIN -->';
+const MARKER_END = '<!-- OPENTOLOGY:CONTEXT:END -->';
 export function generateContextSection(projectId, graphUri) {
     const contextUri = `${graphUri}/context`;
     const sessionsUri = `${graphUri}/sessions`;

package/dist/templates/otx-ontology.d.ts

@@ -1,2 +1 @@
 export declare const OTX_BOOTSTRAP_TURTLE = "@prefix otx: <https://opentology.dev/vocab#> .\n@prefix owl: <http://www.w3.org/2002/07/owl#> .\n@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n\notx:Project a owl:Class .\notx:Decision a owl:Class .\notx:Issue a owl:Class .\notx:Knowledge a owl:Class .\notx:Session a owl:Class .\notx:Pattern a owl:Class .\notx:Module a owl:Class .\n\notx:title a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:date a owl:DatatypeProperty ; rdfs:range xsd:date .\notx:body a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:status a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:reason a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:cause a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:solution a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:nextTodo a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:relatedTo a owl:ObjectProperty .\notx:project a owl:ObjectProperty .\notx:dependsOn a owl:ObjectProperty ; rdfs:domain otx:Module ; rdfs:range otx:Module .\notx:stack a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:alternative a owl:DatatypeProperty ; rdfs:range xsd:string .\n\notx:Class a owl:Class .\notx:Interface a owl:Class .\notx:Function a owl:Class .\notx:Method a owl:Class .\n\notx:definedIn a owl:ObjectProperty ; rdfs:range otx:Module .\notx:extends a owl:ObjectProperty ; rdfs:domain otx:Class ; rdfs:range otx:Class .\notx:implements a owl:ObjectProperty ; rdfs:domain otx:Class ; rdfs:range otx:Interface .\notx:hasMethod a owl:ObjectProperty ; rdfs:domain otx:Class ; rdfs:range otx:Method .\notx:calls a owl:ObjectProperty ; rdfs:domain otx:Method ; rdfs:range otx:Method .\notx:returns a owl:DatatypeProperty ; rdfs:range xsd:string .\notx:paramType a owl:DatatypeProperty ; rdfs:range xsd:string .\n";
-export declare function buildAskQuery(contextGraphUri: string): string;

package/dist/templates/otx-ontology.js

@@ -39,6 +39,3 @@ otx:calls a owl:ObjectProperty ; rdfs:domain otx:Method ; rdfs:range otx:Method
 otx:returns a owl:DatatypeProperty ; rdfs:range xsd:string .
 otx:paramType a owl:DatatypeProperty ; rdfs:range xsd:string .
 `;
-export function buildAskQuery(contextGraphUri) {
-    return `ASK { GRAPH <${contextGraphUri}> { <https://opentology.dev/vocab#Decision> a <http://www.w3.org/2002/07/owl#Class> } }`;
-}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "opentology",
-  "version": "0.2.3",
+  "version": "0.2.4",
   "description": "CLI-managed RDF/SPARQL infrastructure — Supabase for RDF",
   "type": "module",
   "bin": {