symbiote-cli 0.1.0

package/dist/src/cortex/stage-4-types.js

@@ -0,0 +1,462 @@
+import { readFileSync } from 'node:fs';
+import { resolve } from 'node:path';
+import { createRequire } from 'node:module';
+import { getGrammar } from '#core/languages.js';
+const cjsRequire = createRequire(import.meta.url);
+const Parser = cjsRequire('tree-sitter');
+export async function runStage4(repo, rootDir, options) {
+    const start = Date.now();
+    const errors = [];
+    let filesProcessed = 0;
+    let nodesCreated = 0;
+    let edgesCreated = 0;
+    const allFiles = options?.force
+        ? await repo.getAllFileNodes()
+        : await repo.getFilesByMaxDepth(4);
+    const files = options?.force ? allFiles : allFiles.filter((f) => f.depthLevel >= 3);
+    const targetSet = options?.targetFiles ? new Set(options.targetFiles) : null;
+    for (const file of files) {
+        if (targetSet && !targetSet.has(file.path))
+            continue;
+        if (!file.language)
+            continue;
+        if (!isJsTs(file.language))
+            continue;
+        const absPath = resolve(rootDir, file.path);
+        let content;
+        try {
+            content = readFileSync(absPath, 'utf-8');
+        }
+        catch (err) {
+            errors.push({
+                filePath: file.path,
+                stage: 4,
+                message: err instanceof Error ? err.message : String(err),
+            });
+            continue;
+        }
+        const grammar = getGrammar(file.language);
+        if (!grammar)
+            continue;
+        try {
+            const functions = await repo.getFunctionsByFile(file.path);
+            const methods = await repo.getMethodsByFile(file.path);
+            const existingVars = await repo.getVariablesByFile(file.path);
+            const existingVarIds = new Set(existingVars.map((v) => v.id));
+            const fileId = `file:${file.path}`;
+            const symbolTable = await repo.getSymbolTable(fileId);
+            const seed = extractTypeInfo(content, grammar, file, functions, methods, existingVarIds, symbolTable);
+            await repo.deleteTypeConstraintsForFile(file.path);
+            await repo.deleteGenericInstantiationsForFile(file.path);
+            if (seed.newVariables.length > 0) {
+                await repo.insertVariableNodes(seed.newVariables);
+                nodesCreated += seed.newVariables.length;
+            }
+            if (seed.newContainsEdges.length > 0) {
+                await repo.insertContainsEdges(seed.newContainsEdges);
+                edgesCreated += seed.newContainsEdges.length;
+            }
+            if (seed.constraints.length > 0) {
+                await repo.insertTypeConstraints(seed.constraints);
+            }
+            if (seed.generics.length > 0) {
+                await repo.insertGenericInstantiations(seed.generics);
+            }
+            if (seed.implementsEdges.length > 0) {
+                await repo.insertImplementsEdges(seed.implementsEdges);
+                edgesCreated += seed.implementsEdges.length;
+            }
+            const propagated = await propagateTypes(repo, file.path, seed.constraints);
+            if (propagated.length > 0) {
+                await repo.insertTypeConstraints(propagated);
+            }
+            const allConstraints = [...seed.constraints, ...propagated];
+            await updateVariableTypes(repo, file.path, allConstraints);
+            await refineCallEdges(repo, file.path, allConstraints);
+            await repo.upsertFileNode({ ...file, depthLevel: 4 });
+            filesProcessed++;
+        }
+        catch (err) {
+            errors.push({
+                filePath: file.path,
+                stage: 4,
+                message: err instanceof Error ? err.message : String(err),
+            });
+        }
+    }
+    return {
+        stage: 4,
+        filesProcessed,
+        nodesCreated,
+        edgesCreated,
+        durationMs: Date.now() - start,
+        errors,
+    };
+}
+function isJsTs(language) {
+    return language === 'javascript' || language === 'typescript' || language === 'tsx';
+}
+function extractTypeInfo(content, grammar, file, functions, methods, existingVarIds, symbolTable) {
+    const parser = new Parser();
+    parser.setLanguage(grammar);
+    const tree = parser.parse(content);
+    const root = tree.rootNode;
+    const constraints = [];
+    const generics = [];
+    const newVariables = [];
+    const newContainsEdges = [];
+    const implementsEdges = [];
+    const relPath = file.path;
+    const fileId = `file:${relPath}`;
+    const fnMap = new Map(functions.map((f) => [f.name, f]));
+    const methodMap = new Map(methods.map((m) => [m.qualifiedName, m]));
+    const cursor = root.walk();
+    let done = false;
+    while (!done) {
+        const node = cursor.currentNode;
+        if (node.type === 'function_declaration' || node.type === 'method_definition') {
+            extractFunctionAnnotations(node, relPath, fnMap, methodMap, constraints);
+        }
+        if (node.type === 'class_declaration' || node.type === 'class') {
+            extractGenericImplements(node, relPath, implementsEdges);
+        }
+        if (node.type === 'lexical_declaration' || node.type === 'variable_declaration') {
+            extractVariableTypeInfo(node, relPath, fileId, existingVarIds, symbolTable, constraints, generics, newVariables, newContainsEdges);
+        }
+        if (cursor.gotoFirstChild())
+            continue;
+        if (cursor.gotoNextSibling())
+            continue;
+        while (true) {
+            if (!cursor.gotoParent()) {
+                done = true;
+                break;
+            }
+            if (cursor.gotoNextSibling())
+                break;
+        }
+    }
+    return { constraints, generics, newVariables, newContainsEdges, implementsEdges };
+}
+function extractFunctionAnnotations(node, relPath, fnMap, methodMap, constraints) {
+    const nameNode = node.childForFieldName('name');
+    if (!nameNode)
+        return;
+    const name = nameNode.text;
+    const isMethod = node.type === 'method_definition';
+    let symbolId;
+    if (isMethod) {
+        const classNode = findParentClass(node);
+        if (!classNode)
+            return;
+        const className = classNode.childForFieldName('name')?.text;
+        if (!className)
+            return;
+        const qualifiedName = `${className}.${name}`;
+        const method = methodMap.get(qualifiedName);
+        if (!method)
+            return;
+        symbolId = method.id;
+    }
+    else {
+        const fn = fnMap.get(name);
+        if (!fn)
+            return;
+        symbolId = fn.id;
+    }
+    const params = node.childForFieldName('parameters');
+    if (params) {
+        extractParameterAnnotations(params, symbolId, relPath, constraints);
+    }
+    const returnType = node.childForFieldName('return_type');
+    if (returnType) {
+        const typeName = returnType.text.replace(/^:\s*/, '');
+        constraints.push({
+            symbolId,
+            typeName,
+            source: 'return_type',
+            confidence: 0.95,
+            filePath: relPath,
+            line: returnType.startPosition.row + 1,
+        });
+    }
+}
+function extractParameterAnnotations(params, symbolId, relPath, constraints) {
+    for (const param of params.children) {
+        if (param.type === 'required_parameter' || param.type === 'optional_parameter') {
+            const typeAnnotation = param.childForFieldName('type') ??
+                param.children.find((c) => c.type === 'type_annotation');
+            if (typeAnnotation) {
+                const typeName = typeAnnotation.text.replace(/^:\s*/, '');
+                constraints.push({
+                    symbolId,
+                    typeName,
+                    source: 'annotation',
+                    confidence: 0.95,
+                    filePath: relPath,
+                    line: param.startPosition.row + 1,
+                });
+            }
+        }
+    }
+}
+function extractVariableTypeInfo(node, relPath, fileId, existingVarIds, symbolTable, constraints, generics, newVariables, newContainsEdges) {
+    for (const child of node.children) {
+        if (child.type !== 'variable_declarator')
+            continue;
+        const nameNode = child.childForFieldName('name');
+        if (!nameNode)
+            continue;
+        const name = nameNode.text;
+        const varId = `var:${relPath}:${name}`;
+        const line = child.startPosition.row + 1;
+        if (!existingVarIds.has(varId)) {
+            const isExported = isNodeExported(node);
+            const typeAnnotation = child.childForFieldName('type');
+            const inferredType = typeAnnotation ? typeAnnotation.text.replace(/^:\s*/, '') : null;
+            newVariables.push({
+                id: varId,
+                name,
+                scope: 'module',
+                filePath: relPath,
+                lineStart: line,
+                lineEnd: child.endPosition.row + 1,
+                isExported,
+                inferredType,
+            });
+            newContainsEdges.push({
+                sourceId: fileId,
+                targetId: varId,
+                confidence: 1.0,
+                stage: 4,
+                reason: null,
+            });
+            existingVarIds.add(varId);
+        }
+        const typeAnnotation = child.childForFieldName('type');
+        if (typeAnnotation) {
+            const typeName = typeAnnotation.text.replace(/^:\s*/, '');
+            constraints.push({
+                symbolId: varId,
+                typeName,
+                source: 'annotation',
+                confidence: 0.95,
+                filePath: relPath,
+                line,
+            });
+        }
+        const valueNode = child.childForFieldName('value');
+        if (!valueNode)
+            continue;
+        if (valueNode.type === 'new_expression') {
+            extractNewExpression(valueNode, varId, relPath, line, symbolTable, constraints, generics);
+        }
+    }
+}
+function extractNewExpression(node, varId, relPath, line, _symbolTable, constraints, generics) {
+    const ctorNode = node.childForFieldName('constructor') ??
+        node.children.find((c) => c.type === 'identifier' || c.type === 'type_identifier');
+    if (!ctorNode)
+        return;
+    const className = ctorNode.text;
+    constraints.push({
+        symbolId: varId,
+        typeName: className,
+        source: 'constructor',
+        confidence: 0.9,
+        filePath: relPath,
+        line,
+    });
+    const typeArgs = node.children.find((c) => c.type === 'type_arguments');
+    if (typeArgs) {
+        const args = [];
+        for (const typeArg of typeArgs.children) {
+            if (typeArg.type === 'type_identifier' ||
+                typeArg.type === 'predefined_type' ||
+                typeArg.type === 'generic_type') {
+                args.push(typeArg.text);
+            }
+        }
+        if (args.length > 0) {
+            generics.push({
+                symbolId: varId,
+                genericName: className,
+                typeArguments: args,
+                filePath: relPath,
+                line,
+            });
+        }
+    }
+}
+function extractGenericImplements(classNode, relPath, implementsEdges) {
+    const className = classNode.childForFieldName('name')?.text;
+    if (!className)
+        return;
+    const classId = `class:${relPath}:${className}`;
+    for (const child of classNode.children) {
+        if (child.type !== 'class_heritage')
+            continue;
+        for (const clause of child.children) {
+            if (clause.type !== 'implements_clause')
+                continue;
+            for (const typeRef of clause.children) {
+                if (typeRef.type === 'generic_type') {
+                    const nameNode = typeRef.children.find((c) => c.type === 'identifier' || c.type === 'type_identifier');
+                    if (nameNode) {
+                        implementsEdges.push({
+                            sourceId: classId,
+                            targetId: `interface:${relPath}:${nameNode.text}`,
+                            line: clause.startPosition.row + 1,
+                            confidence: 1.0,
+                            stage: 4,
+                            reason: 'generic_implements',
+                        });
+                    }
+                }
+            }
+        }
+    }
+}
+function findParentClass(node) {
+    let parent = node.parent;
+    while (parent) {
+        if (parent.type === 'class_declaration' || parent.type === 'class') {
+            return parent;
+        }
+        parent = parent.parent;
+    }
+    return null;
+}
+function isNodeExported(node) {
+    const parent = node.parent;
+    if (parent?.type === 'export_statement')
+        return true;
+    const grandparent = parent?.parent;
+    if (grandparent?.type === 'export_statement')
+        return true;
+    return false;
+}
+async function propagateTypes(repo, filePath, seedConstraints) {
+    const propagated = [];
+    const seen = new Set();
+    for (const c of seedConstraints) {
+        seen.add(`${c.symbolId}:${c.typeName}`);
+    }
+    const worklist = [];
+    const functions = await repo.getFunctionsByFile(filePath);
+    const methods = await repo.getMethodsByFile(filePath);
+    const variables = await repo.getVariablesByFile(filePath);
+    const returnTypeByFn = new Map();
+    for (const c of seedConstraints) {
+        if (c.source === 'return_type') {
+            returnTypeByFn.set(c.symbolId, c.typeName);
+        }
+    }
+    const ctorTypeByVar = new Map();
+    for (const c of seedConstraints) {
+        if (c.source === 'constructor') {
+            ctorTypeByVar.set(c.symbolId, c.typeName);
+        }
+    }
+    for (const v of variables) {
+        const calls = await repo.getCallsFrom(v.id);
+        if (calls.length > 0)
+            continue;
+    }
+    for (const fn of [...functions, ...methods]) {
+        const calls = await repo.getCallsFrom(fn.id);
+        for (const call of calls) {
+            const returnType = returnTypeByFn.get(call.targetId);
+            if (!returnType)
+                continue;
+            const assignedVars = variables.filter((v) => {
+                const varLine = v.lineStart;
+                return varLine >= fn.lineStart && varLine <= fn.lineEnd;
+            });
+            for (const v of assignedVars) {
+                const key = `${v.id}:${returnType}`;
+                if (seen.has(key))
+                    continue;
+                seen.add(key);
+                const item = {
+                    symbolId: v.id,
+                    typeName: returnType,
+                    confidence: 0.8,
+                    source: 'assignment',
+                    filePath,
+                    line: v.lineStart,
+                };
+                worklist.push(item);
+            }
+        }
+    }
+    for (const fn of functions) {
+        const returnType = returnTypeByFn.get(fn.id);
+        if (!returnType)
+            continue;
+        const callsTo = await repo.getCallsTo(fn.id);
+        for (const call of callsTo) {
+            const callerFn = functions.find((f) => f.id === call.sourceId);
+            if (!callerFn)
+                continue;
+            const innerVars = variables.filter((v) => v.lineStart >= callerFn.lineStart && v.lineStart <= callerFn.lineEnd);
+            for (const v of innerVars) {
+                const key = `${v.id}:${returnType}`;
+                if (seen.has(key))
+                    continue;
+                seen.add(key);
+                worklist.push({
+                    symbolId: v.id,
+                    typeName: returnType,
+                    confidence: 0.75,
+                    source: 'assignment',
+                    filePath,
+                    line: v.lineStart,
+                });
+            }
+        }
+    }
+    while (worklist.length > 0) {
+        const item = worklist.pop();
+        propagated.push({
+            symbolId: item.symbolId,
+            typeName: item.typeName,
+            source: item.source,
+            confidence: item.confidence,
+            filePath: item.filePath,
+            line: item.line,
+        });
+    }
+    return propagated;
+}
+async function updateVariableTypes(repo, _filePath, allConstraints) {
+    const bySymbol = new Map();
+    for (const c of allConstraints) {
+        if (!c.symbolId.startsWith('var:'))
+            continue;
+        const list = bySymbol.get(c.symbolId) ?? [];
+        list.push(c);
+        bySymbol.set(c.symbolId, list);
+    }
+    for (const [symbolId, constraints] of bySymbol) {
+        constraints.sort((a, b) => b.confidence - a.confidence);
+        const best = constraints[0];
+        await repo.updateVariableType(symbolId, best.typeName);
+    }
+}
+async function refineCallEdges(repo, filePath, allConstraints) {
+    const functions = await repo.getFunctionsByFile(filePath);
+    const methods = await repo.getMethodsByFile(filePath);
+    for (const fn of [...functions, ...methods]) {
+        const calls = await repo.getCallsFrom(fn.id);
+        for (const call of calls) {
+            if (call.confidence >= 0.9)
+                continue;
+            const hasTypeInfo = allConstraints.some((c) => c.symbolId === call.sourceId || c.symbolId === call.targetId);
+            if (hasTypeInfo && call.confidence < 0.7) {
+                await repo.updateCallEdgeConfidence(call.sourceId, call.targetId, 0.7, 'type-refined');
+            }
+        }
+    }
+}
+//# sourceMappingURL=stage-4-types.js.map

package/dist/src/cortex/stage-4-types.js.map

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package/dist/src/cortex/stage-5-flow.d.ts

@@ -0,0 +1,7 @@
+import { CortexRepository } from './repository.js';
+import type { StageResult } from './types.js';
+export declare function runStage5(repo: CortexRepository, rootDir: string, options?: {
+    force?: boolean;
+    targetFiles?: string[];
+}): Promise<StageResult>;
+//# sourceMappingURL=stage-5-flow.d.ts.map

package/dist/src/cortex/stage-5-flow.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"stage-5-flow.d.ts","sourceRoot":"","sources":["../../../src/cortex/stage-5-flow.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,KAAK,EACR,WAAW,EAUd,MAAM,YAAY,CAAC;AAoCpB,wBAAsB,SAAS,CAC3B,IAAI,EAAE,gBAAgB,EACtB,OAAO,EAAE,MAAM,EACf,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAA;CAAE,GACtD,OAAO,CAAC,WAAW,CAAC,CA+HtB"}