@gsep/core 0.8.0

package/dist/gene-bank/adapters/InMemoryGeneStorage.js

@@ -0,0 +1,115 @@
+export class InMemoryGeneStorage {
+    genes = new Map();
+    adoptions = new Map();
+    async store(gene) {
+        this.genes.set(gene.id, gene);
+    }
+    async get(geneId) {
+        return this.genes.get(geneId) || null;
+    }
+    async update(gene) {
+        if (!this.genes.has(gene.id)) {
+            throw new Error(`Gene not found: ${gene.id}`);
+        }
+        this.genes.set(gene.id, gene);
+    }
+    async delete(geneId) {
+        this.genes.delete(geneId);
+        this.adoptions.delete(geneId);
+    }
+    async search(filters) {
+        let results = Array.from(this.genes.values());
+        if (filters.tenantId) {
+            results = results.filter(g => g.tenant.tenantId === filters.tenantId);
+        }
+        if (filters.type && filters.type.length > 0) {
+            results = results.filter(g => filters.type.includes(g.type));
+        }
+        if (filters.domain && filters.domain.length > 0) {
+            results = results.filter(g => filters.domain.includes(g.domain));
+        }
+        if (filters.tags && filters.tags.length > 0) {
+            results = results.filter(g => filters.tags.some(tag => g.tags.includes(tag)));
+        }
+        if (filters.minFitness !== undefined) {
+            results = results.filter(g => g.fitness.overallFitness >= filters.minFitness);
+        }
+        const sortBy = filters.sortBy || 'fitness';
+        const sortOrder = filters.sortOrder || 'desc';
+        if (sortBy === 'fitness') {
+            results.sort((a, b) => {
+                const diff = a.fitness.overallFitness - b.fitness.overallFitness;
+                return sortOrder === 'desc' ? -diff : diff;
+            });
+        }
+        else if (sortBy === 'adoptions') {
+            results.sort((a, b) => {
+                const diff = a.fitness.adoptionCount - b.fitness.adoptionCount;
+                return sortOrder === 'desc' ? -diff : diff;
+            });
+        }
+        else if (sortBy === 'createdAt') {
+            results.sort((a, b) => {
+                const diff = new Date(a.createdAt).getTime() - new Date(b.createdAt).getTime();
+                return sortOrder === 'desc' ? -diff : diff;
+            });
+        }
+        else if (sortBy === 'updatedAt') {
+            results.sort((a, b) => {
+                const diff = new Date(a.updatedAt).getTime() - new Date(b.updatedAt).getTime();
+                return sortOrder === 'desc' ? -diff : diff;
+            });
+        }
+        const limit = filters.limit || 10;
+        return results.slice(0, limit);
+    }
+    async listByTenant(tenantId, scope) {
+        let results = Array.from(this.genes.values())
+            .filter(g => g.tenant.tenantId === tenantId);
+        if (scope) {
+            results = results.filter(g => g.tenant.scope === scope);
+        }
+        return results;
+    }
+    async getLineage(geneId) {
+        const gene = this.genes.get(geneId);
+        if (!gene)
+            return [];
+        const lineage = [];
+        let currentGeneId = gene.lineage.parentGeneId;
+        while (currentGeneId) {
+            const parent = this.genes.get(currentGeneId);
+            if (!parent)
+                break;
+            lineage.push(parent);
+            currentGeneId = parent.lineage.parentGeneId;
+        }
+        return lineage;
+    }
+    async recordAdoption(geneId, agentId, performance) {
+        if (!this.adoptions.has(geneId)) {
+            this.adoptions.set(geneId, []);
+        }
+        this.adoptions.get(geneId).push({ agentId, performance });
+        const gene = this.genes.get(geneId);
+        if (gene) {
+            gene.fitness.adoptionCount++;
+            const adoptions = this.adoptions.get(geneId);
+            const avgPerformance = adoptions.reduce((sum, a) => sum + a.performance, 0) / adoptions.length;
+            gene.fitness.adoptionPerformance = avgPerformance;
+            gene.updatedAt = new Date().toISOString();
+        }
+    }
+    getStats() {
+        return {
+            totalGenes: this.genes.size,
+            totalAdoptions: Array.from(this.adoptions.values())
+                .reduce((sum, adoptions) => sum + adoptions.length, 0),
+        };
+    }
+    clear() {
+        this.genes.clear();
+        this.adoptions.clear();
+    }
+}
+//# sourceMappingURL=InMemoryGeneStorage.js.map

package/dist/gene-bank/adapters/InMemoryGeneStorage.js.map

@@ -0,0 +1 @@
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package/dist/gene-bank/adapters/PostgresGeneStorage.d.ts

@@ -0,0 +1,21 @@
+import type { CognitiveGene } from '../CognitiveGene';
+import type { GeneStorageAdapter, GeneSearchFilters } from '../GeneBank';
+export interface PostgresConnection {
+    query(sql: string, params?: any[]): Promise<{
+        rows: any[];
+    }>;
+}
+export declare class PostgresGeneStorage implements GeneStorageAdapter {
+    private connection;
+    constructor(connection: PostgresConnection);
+    store(gene: CognitiveGene): Promise<void>;
+    get(geneId: string): Promise<CognitiveGene | null>;
+    update(gene: CognitiveGene): Promise<void>;
+    delete(geneId: string): Promise<void>;
+    search(filters: GeneSearchFilters): Promise<CognitiveGene[]>;
+    listByTenant(tenantId: string, scope?: string): Promise<CognitiveGene[]>;
+    getLineage(geneId: string): Promise<CognitiveGene[]>;
+    recordAdoption(geneId: string, agentId: string, performance: number): Promise<void>;
+    private rowToGene;
+}
+//# sourceMappingURL=PostgresGeneStorage.d.ts.map

package/dist/gene-bank/adapters/PostgresGeneStorage.d.ts.map

@@ -0,0 +1 @@
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package/dist/gene-bank/adapters/PostgresGeneStorage.js

@@ -0,0 +1,272 @@
+export class PostgresGeneStorage {
+    connection;
+    constructor(connection) {
+        this.connection = connection;
+    }
+    async store(gene) {
+        await this.connection.query(`
+            INSERT INTO cognitive_genes (
+                id, version, name, description, type, domain,
+                fitness,
+                parent_gene_id, generation, ancestors, mutation_history,
+                instruction, examples, required_capabilities,
+                applicable_contexts, contraindications, content_metadata,
+                tenant_id, created_by, scope, verified,
+                created_at, updated_at, tags
+            ) VALUES (
+                $1, $2, $3, $4, $5, $6,
+                $7::jsonb,
+                $8, $9, $10::jsonb, $11::jsonb,
+                $12, $13::jsonb, $14::jsonb,
+                $15::jsonb, $16::jsonb, $17::jsonb,
+                $18, $19, $20, $21,
+                $22, $23, $24::jsonb
+            )
+            `, [
+            gene.id,
+            gene.version,
+            gene.name,
+            gene.description,
+            gene.type,
+            gene.domain,
+            JSON.stringify(gene.fitness),
+            gene.lineage.parentGeneId,
+            gene.lineage.generation,
+            JSON.stringify(gene.lineage.ancestors),
+            JSON.stringify(gene.lineage.mutationHistory),
+            gene.content.instruction,
+            JSON.stringify(gene.content.examples || []),
+            JSON.stringify(gene.content.requiredCapabilities || []),
+            JSON.stringify(gene.content.applicableContexts || []),
+            JSON.stringify(gene.content.contraindications || []),
+            JSON.stringify(gene.content.metadata || {}),
+            gene.tenant.tenantId,
+            gene.tenant.createdBy,
+            gene.tenant.scope,
+            gene.tenant.verified,
+            gene.createdAt,
+            gene.updatedAt,
+            JSON.stringify(gene.tags),
+        ]);
+    }
+    async get(geneId) {
+        const result = await this.connection.query('SELECT * FROM cognitive_genes WHERE id = $1', [geneId]);
+        if (result.rows.length === 0) {
+            return null;
+        }
+        return this.rowToGene(result.rows[0]);
+    }
+    async update(gene) {
+        await this.connection.query(`
+            UPDATE cognitive_genes SET
+                version = $2,
+                name = $3,
+                description = $4,
+                type = $5,
+                domain = $6,
+                fitness = $7::jsonb,
+                parent_gene_id = $8,
+                generation = $9,
+                ancestors = $10::jsonb,
+                mutation_history = $11::jsonb,
+                instruction = $12,
+                examples = $13::jsonb,
+                required_capabilities = $14::jsonb,
+                applicable_contexts = $15::jsonb,
+                contraindications = $16::jsonb,
+                content_metadata = $17::jsonb,
+                tenant_id = $18,
+                created_by = $19,
+                scope = $20,
+                verified = $21,
+                updated_at = $22,
+                tags = $23::jsonb
+            WHERE id = $1
+            `, [
+            gene.id,
+            gene.version,
+            gene.name,
+            gene.description,
+            gene.type,
+            gene.domain,
+            JSON.stringify(gene.fitness),
+            gene.lineage.parentGeneId,
+            gene.lineage.generation,
+            JSON.stringify(gene.lineage.ancestors),
+            JSON.stringify(gene.lineage.mutationHistory),
+            gene.content.instruction,
+            JSON.stringify(gene.content.examples || []),
+            JSON.stringify(gene.content.requiredCapabilities || []),
+            JSON.stringify(gene.content.applicableContexts || []),
+            JSON.stringify(gene.content.contraindications || []),
+            JSON.stringify(gene.content.metadata || {}),
+            gene.tenant.tenantId,
+            gene.tenant.createdBy,
+            gene.tenant.scope,
+            gene.tenant.verified,
+            gene.updatedAt,
+            JSON.stringify(gene.tags),
+        ]);
+    }
+    async delete(geneId) {
+        await this.connection.query('DELETE FROM cognitive_genes WHERE id = $1', [geneId]);
+    }
+    async search(filters) {
+        const conditions = [];
+        const params = [];
+        let paramIndex = 1;
+        if (filters.tenantId) {
+            conditions.push(`tenant_id = $${paramIndex++}`);
+            params.push(filters.tenantId);
+        }
+        if (filters.type && filters.type.length > 0) {
+            conditions.push(`type = ANY($${paramIndex++})`);
+            params.push(filters.type);
+        }
+        if (filters.domain && filters.domain.length > 0) {
+            conditions.push(`domain = ANY($${paramIndex++})`);
+            params.push(filters.domain);
+        }
+        if (filters.minFitness !== undefined) {
+            conditions.push(`(fitness->>'overallFitness')::numeric >= $${paramIndex++}`);
+            params.push(filters.minFitness);
+        }
+        if (filters.minAdoptions !== undefined) {
+            conditions.push(`(fitness->>'adoptionCount')::integer >= $${paramIndex++}`);
+            params.push(filters.minAdoptions);
+        }
+        if (filters.scope && filters.scope.length > 0) {
+            conditions.push(`scope = ANY($${paramIndex++})`);
+            params.push(filters.scope);
+        }
+        if (filters.verifiedOnly) {
+            conditions.push('verified = TRUE');
+        }
+        if (filters.tags && filters.tags.length > 0) {
+            conditions.push(`tags ?| $${paramIndex++}`);
+            params.push(filters.tags);
+        }
+        const whereClause = conditions.length > 0
+            ? `WHERE ${conditions.join(' AND ')}`
+            : '';
+        const sortBy = filters.sortBy || 'fitness';
+        const sortOrder = filters.sortOrder?.toLowerCase() === 'asc' ? 'ASC' : 'DESC';
+        let orderBy = '';
+        switch (sortBy) {
+            case 'fitness':
+                orderBy = `(fitness->>'overallFitness')::numeric ${sortOrder.toUpperCase()}`;
+                break;
+            case 'adoptions':
+                orderBy = `(fitness->>'adoptionCount')::integer ${sortOrder.toUpperCase()}`;
+                break;
+            case 'createdAt':
+                orderBy = `created_at ${sortOrder.toUpperCase()}`;
+                break;
+            case 'updatedAt':
+                orderBy = `updated_at ${sortOrder.toUpperCase()}`;
+                break;
+            default:
+                orderBy = `created_at DESC`;
+        }
+        const limit = filters.limit || 10;
+        const offset = filters.offset || 0;
+        const sql = `
+            SELECT * FROM cognitive_genes
+            ${whereClause}
+            ORDER BY ${orderBy}
+            LIMIT $${paramIndex++} OFFSET $${paramIndex++}
+        `;
+        params.push(limit, offset);
+        const result = await this.connection.query(sql, params);
+        return result.rows.map(row => this.rowToGene(row));
+    }
+    async listByTenant(tenantId, scope) {
+        const sql = scope
+            ? 'SELECT * FROM cognitive_genes WHERE tenant_id = $1 AND scope = $2'
+            : 'SELECT * FROM cognitive_genes WHERE tenant_id = $1';
+        const params = scope ? [tenantId, scope] : [tenantId];
+        const result = await this.connection.query(sql, params);
+        return result.rows.map(row => this.rowToGene(row));
+    }
+    async getLineage(geneId) {
+        const sql = `
+            WITH RECURSIVE gene_lineage AS (
+                -- Base case: the gene itself
+                SELECT * FROM cognitive_genes WHERE id = $1
+
+                UNION ALL
+
+                -- Recursive case: parent genes
+                SELECT g.*
+                FROM cognitive_genes g
+                INNER JOIN gene_lineage gl ON g.id = gl.parent_gene_id
+            )
+            SELECT * FROM gene_lineage
+            WHERE id != $1
+            ORDER BY generation DESC
+        `;
+        const result = await this.connection.query(sql, [geneId]);
+        return result.rows.map(row => this.rowToGene(row));
+    }
+    async recordAdoption(geneId, agentId, performance) {
+        await this.connection.query(`
+            INSERT INTO gene_adoptions (gene_id, agent_id, performance)
+            VALUES ($1, $2, $3)
+            `, [geneId, agentId, performance]);
+        const adoptionsResult = await this.connection.query(`
+            SELECT COUNT(*)::integer as count, AVG(performance)::numeric as avg_performance
+            FROM gene_adoptions
+            WHERE gene_id = $1
+            `, [geneId]);
+        const { count, avg_performance } = adoptionsResult.rows[0];
+        await this.connection.query(`
+            UPDATE cognitive_genes
+            SET fitness = jsonb_set(
+                    jsonb_set(
+                        fitness,
+                        '{adoptionCount}',
+                        $2::text::jsonb
+                    ),
+                    '{adoptionPerformance}',
+                    $3::text::jsonb
+                ),
+                updated_at = NOW()
+            WHERE id = $1
+            `, [geneId, count, avg_performance]);
+    }
+    rowToGene(row) {
+        return {
+            id: row.id,
+            version: row.version,
+            name: row.name,
+            description: row.description,
+            type: row.type,
+            domain: row.domain,
+            fitness: row.fitness,
+            lineage: {
+                parentGeneId: row.parent_gene_id,
+                generation: row.generation,
+                ancestors: row.ancestors,
+                mutationHistory: row.mutation_history,
+            },
+            content: {
+                instruction: row.instruction,
+                examples: row.examples,
+                requiredCapabilities: row.required_capabilities,
+                applicableContexts: row.applicable_contexts,
+                contraindications: row.contraindications,
+                metadata: row.content_metadata,
+            },
+            tenant: {
+                tenantId: row.tenant_id,
+                createdBy: row.created_by,
+                scope: row.scope,
+                verified: row.verified,
+            },
+            createdAt: row.created_at.toISOString(),
+            updatedAt: row.updated_at.toISOString(),
+            tags: row.tags,
+        };
+    }
+}
+//# sourceMappingURL=PostgresGeneStorage.js.map

package/dist/gene-bank/adapters/PostgresGeneStorage.js.map

@@ -0,0 +1 @@
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package/dist/gene-bank/index.d.ts

@@ -0,0 +1,8 @@
+export { CognitiveGene, GeneType, GeneContent, FitnessMetrics, Lineage, TenantInfo, SharingScope, GeneExtractionResult, GeneAdoptionResult, CognitiveGeneSchema, GeneTypeSchema, GeneContentSchema, FitnessMetricsSchema, LineageSchema, TenantInfoSchema, SharingScopeSchema, GeneExtractionResultSchema, GeneAdoptionResultSchema, createGeneId, meetsMinimumFitness, calculateFitnessDelta, isMarketplaceReady, } from './CognitiveGene';
+export { GeneBank, GeneBankConfig, GeneBankConfigSchema, GeneBankStats, GeneStorageAdapter, GeneSearchFilters, GeneSearchFiltersSchema, } from './GeneBank';
+export { GeneExtractor, GeneExtractionConfig, GeneExtractionConfigSchema, MutationContext, } from './GeneExtractor';
+export { GeneMatcher, GeneMatchConfig, GeneMatchConfigSchema, MatchContext, GeneMatchResult, } from './GeneMatcher';
+export { SandboxTester, SandboxConfig, SandboxConfigSchema, SandboxTestCase, TestCaseResult, SandboxTestResult, BaselinePerformance, } from './SandboxTester';
+export { GeneAdopter, GeneAdoptionConfig, GeneAdoptionConfigSchema, AdoptionRequest, AdoptedGeneStatus, } from './GeneAdopter';
+export { MarketplaceClient } from './MarketplaceClient';
+//# sourceMappingURL=index.d.ts.map

package/dist/gene-bank/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/gene-bank/index.js

@@ -0,0 +1,8 @@
+export { CognitiveGeneSchema, GeneTypeSchema, GeneContentSchema, FitnessMetricsSchema, LineageSchema, TenantInfoSchema, SharingScopeSchema, GeneExtractionResultSchema, GeneAdoptionResultSchema, createGeneId, meetsMinimumFitness, calculateFitnessDelta, isMarketplaceReady, } from './CognitiveGene';
+export { GeneBank, GeneBankConfigSchema, GeneSearchFiltersSchema, } from './GeneBank';
+export { GeneExtractor, GeneExtractionConfigSchema, } from './GeneExtractor';
+export { GeneMatcher, GeneMatchConfigSchema, } from './GeneMatcher';
+export { SandboxTester, SandboxConfigSchema, } from './SandboxTester';
+export { GeneAdopter, GeneAdoptionConfigSchema, } from './GeneAdopter';
+export { MarketplaceClient } from './MarketplaceClient';
+//# sourceMappingURL=index.js.map

package/dist/gene-bank/index.js.map

@@ -0,0 +1 @@
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package/dist/immune/BehavioralImmuneSystem.d.ts

@@ -0,0 +1,68 @@
+import type { ContentFirewall } from '../firewall/ContentFirewall.js';
+import type { GenomeKernel } from '../core/GenomeKernel.js';
+import type { PurposeSurvival } from '../evolution/PurposeSurvival.js';
+export type OutputThreatType = 'system-prompt-leakage' | 'injection-echo' | 'role-confusion' | 'purpose-deviation' | 'instruction-compliance' | 'data-exfiltration';
+export interface OutputThreat {
+    type: OutputThreatType;
+    severity: 'low' | 'medium' | 'high' | 'critical';
+    evidence: string;
+    description: string;
+}
+export interface ImmuneVerdict {
+    clean: boolean;
+    response: string;
+    threats: OutputThreat[];
+    action: 'pass' | 'sanitize' | 'quarantine';
+    confidence: number;
+}
+export interface ImmuneStatus {
+    totalScans: number;
+    threatsDetected: number;
+    quarantinesTriggered: number;
+    sanitizations: number;
+    lastScanAt: Date | null;
+    immuneMemorySize: number;
+}
+export interface ImmuneMemoryEntry {
+    type: OutputThreatType;
+    evidence: string;
+    timestamp: Date;
+}
+export interface BISConfig {
+    firewall: ContentFirewall;
+    genomeKernel?: GenomeKernel;
+    purposeSurvival?: PurposeSurvival;
+    c0Identity: {
+        purpose: string;
+        constraints: string[];
+        forbiddenTopics: string[];
+    };
+}
+export declare class BehavioralImmuneSystem {
+    private firewall;
+    private genomeKernel?;
+    private purposeSurvival?;
+    private c0Identity;
+    private immuneMemory;
+    private static readonly MAX_MEMORY_SIZE;
+    private totalScans;
+    private threatsDetected;
+    private quarantinesTriggered;
+    private sanitizations;
+    private lastScanAt;
+    constructor(config: BISConfig);
+    scanOutput(response: string, userMessage: string, assembledPrompt: string): ImmuneVerdict;
+    private checkSystemPromptLeakage;
+    private checkInjectionEcho;
+    private checkRoleConfusion;
+    private checkPurposeDeviation;
+    private checkInstructionCompliance;
+    private checkDataExfiltration;
+    quarantineAndRecover(): void;
+    getImmuneStatus(): ImmuneStatus;
+    private classifyAction;
+    private computeConfidence;
+    private sanitizeResponse;
+    private recordInMemory;
+}
+//# sourceMappingURL=BehavioralImmuneSystem.d.ts.map

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