graphrag-knowledge-graph

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This skill should be used when the user asks to "ingest text into graphrag", "add document to knowledge graph", "create entity", "create relationship", "query knowledge graph", "list graph entities", "delete document"

sharpninja By sharpninja schedule Updated 5/26/2026
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name: GraphRAG Knowledge Graph description: This skill should be used when the user asks to "ingest text into graphrag", "add document to knowledge graph", "create entity", "create relationship", "query knowledge graph", "list graph entities", "delete document"

Initialization (Codex)

Call workflow.sessionlog.bootstrap through lib/repl-invoke.sh to initialize the session log subsystem before issuing any workflow commands:

type: request
payload:
  requestId: req-20260409T120000Z-bootstrap-001
  method: workflow.sessionlog.bootstrap
  params: {}

This is idempotent and should be called once per conversation context. If you write to mcpserver-repl --agent-stdio directly for GraphRAG diagnostics, send one single-line JSON request envelope per stdin message.

GraphRAG Knowledge Graph

Overview

To interact with the workspace GraphRAG knowledge graph, use the workflow.graphrag.* REPL command namespace. Direct mcpserver-repl --agent-stdio calls must be single-line JSON request envelopes, not formatted YAML. GraphRAG combines graph-based retrieval with semantic search, enabling richer context retrieval than vector-only approaches.

GraphRAG is disabled by default. Confirm it is active for the workspace before calling any operations — workflow.graphrag.status will report enabled: false if it has not been configured.

Checking GraphRAG Status

To inspect whether GraphRAG is enabled, initialized, and indexed for the active workspace:

type: request
payload:
  requestId: req-20260409T120000Z-status-001
  method: workflow.graphrag.status
  params: {}

type: result
payload:
  requestId: req-20260409T120000Z-status-001
  result:
    enabled: true
    workspacePath: /workspace/my-project
    graphRoot: /workspace/my-project/.graphrag
    state: indexed
    isInitialized: true
    isIndexed: true
    lastIndexedAtUtc: 2026-04-09T10:00:00Z
    lastSuccessAtUtc: 2026-04-09T10:00:00Z
    lastIndexDurationMs: 4200
    lastIndexedDocumentCount: 38
    inputDocumentCount: 38
    backend: internal-fallback

Key state values: disabled, uninitialized, idle, indexing, indexed, error.

Triggering Indexing

To rebuild the GraphRAG index from the current corpus:

type: request
payload:
  requestId: req-20260409T120001Z-index-001
  method: workflow.graphrag.index
  params:
    force: false

Set force: true to rebuild even when no corpus changes are detected. The response reports the post-index status including whether the job was started immediately or queued.

Querying the Knowledge Graph

To run a natural-language query against the indexed graph:

type: request
payload:
  requestId: req-20260409T120002Z-query-001
  method: workflow.graphrag.query
  params:
    query: What authentication mechanisms does the system support?
    mode: local
    maxChunks: 10
    includeContextChunks: true
    maxEntities: 20
    maxRelationships: 20
    communityDepth: 2
    responseTokenBudget: 2000

Valid mode values:

  • local — focuses on directly relevant entities and their immediate relationships; lower latency
  • global — traverses community structure for broad thematic answers; higher coverage
  • drift — follows conceptual drift to surface related but non-obvious connections

All params except query are optional. The result includes an answer, source citations, and optionally the raw chunks, entities, and relationships used:

type: result
payload:
  requestId: req-20260409T120002Z-query-001
  result:
    query: What authentication mechanisms does the system support?
    mode: local
    answer: |
      The system supports API key authentication via the X-Api-Key header,
      workspace-scoped token rotation on server restart, and HMAC-SHA256
      marker signature verification for agent bootstrap.
    citations:
      - sourceKey: docs/MCP-SERVER.md
        chunkId: chunk-0042
        snippet: "API key authentication is required for all /mcpserver/* endpoints..."
    entities:
      - ApiKeyAuthentication
      - HmacSignatureVerification
    relationships:
      - ApiKeyAuthentication -> WorkspaceIsolation
    fallbackUsed: false
    backend: internal-fallback

Ingesting Raw Text

To add a new document to the GraphRAG corpus without triggering a full reindex:

type: request
payload:
  requestId: req-20260409T120003Z-ingest-001
  method: workflow.graphrag.ingest
  params:
    content: |
      JWT Authentication Design

      The token service uses HS256 symmetric signing with a 256-bit workspace key.
      Tokens expire after 1 hour. Refresh tokens use RS256 and expire after 30 days.
      The JwtValidator class validates token signatures and extracts claims.
    title: JWT Authentication Design
    sourceType: adhoc-text
    sourceKey: docs/jwt-auth-design
    triggerReindex: false

Required: content. Optional fields:

  • title — human-readable document name (defaults to a generated ID if omitted)
  • sourceType — classification tag, defaults to adhoc-text
  • sourceKey — unique path/key for the document; defaults to title or a generated ID
  • triggerReindex — when true, starts a full index rebuild after ingestion
type: result
payload:
  requestId: req-20260409T120003Z-ingest-001
  result:
    documentId: doc-a1b2c3d4
    chunkCount: 4
    tokenCount: 312
    sourceType: adhoc-text
    sourceKey: docs/jwt-auth-design
    reindexTriggered: false

Store the returned documentId to manage the document later.

Document Management

Listing Documents

To browse documents in the corpus with pagination:

type: request
payload:
  requestId: req-20260409T120004Z-doclist-001
  method: workflow.graphrag.documents.list
  params:
    skip: 0
    take: 50
    sourceType: adhoc-text

The sourceType filter is optional. The result includes documents (array of summaries) and totalCount:

type: result
payload:
  requestId: req-20260409T120004Z-doclist-001
  result:
    documents:
      - id: doc-a1b2c3d4
        sourceType: adhoc-text
        sourceKey: docs/jwt-auth-design
        ingestedAt: 2026-04-09T12:00:03Z
        contentHash: sha256:abcdef1234...
        chunkCount: 4
        totalTokens: 312
    totalCount: 1

Getting Document Chunks

To inspect the individual text chunks for a specific document:

type: request
payload:
  requestId: req-20260409T120005Z-chunks-001
  method: workflow.graphrag.documents.chunks
  params:
    documentId: doc-a1b2c3d4

type: result
payload:
  requestId: req-20260409T120005Z-chunks-001
  result:
    documentId: doc-a1b2c3d4
    chunks:
      - id: chunk-0001
        content: JWT Authentication Design. The token service uses HS256...
        tokenCount: 78
        chunkIndex: 0
      - id: chunk-0002
        content: Tokens expire after 1 hour. Refresh tokens use RS256...
        tokenCount: 82
        chunkIndex: 1
    totalChunks: 4

Deleting a Document

To remove a document and all its chunks from the corpus:

type: request
payload:
  requestId: req-20260409T120006Z-docdel-001
  method: workflow.graphrag.documents.delete
  params:
    documentId: doc-a1b2c3d4

type: result
payload:
  requestId: req-20260409T120006Z-docdel-001
  result:
    documentId: doc-a1b2c3d4
    chunksRemoved: 4
    success: true

Entity Management

Graph entities represent named concepts, people, organizations, or technical components extracted from or manually added to the corpus.

Creating an Entity

type: request
payload:
  requestId: req-20260409T120007Z-entitycreate-001
  method: workflow.graphrag.entities.create
  params:
    name: TokenService
    entityType: component
    description: Generates and signs JWT tokens using HS256 symmetric keys
    metadata: '{"project":"McpServer","layer":"services"}'

Required: name, entityType. Optional: description, metadata (JSON string).

type: result
payload:
  requestId: req-20260409T120007Z-entitycreate-001
  result:
    id: ent-001
    name: TokenService
    entityType: component
    description: Generates and signs JWT tokens using HS256 symmetric keys
    createdAtUtc: 2026-04-09T12:00:07Z
    updatedAtUtc: 2026-04-09T12:00:07Z

Listing Entities

type: request
payload:
  requestId: req-20260409T120008Z-entitylist-001
  method: workflow.graphrag.entities.list
  params:
    skip: 0
    take: 50
    entityType: component

The entityType filter is optional. Returns entities array and totalCount.

Getting a Single Entity

type: request
payload:
  requestId: req-20260409T120009Z-entityget-001
  method: workflow.graphrag.entities.get
  params:
    entityId: ent-001

Updating an Entity

type: request
payload:
  requestId: req-20260409T120010Z-entityupdate-001
  method: workflow.graphrag.entities.update
  params:
    entityId: ent-001
    name: TokenService
    entityType: component
    description: Generates and signs JWT tokens; supports HS256 and RS256 algorithms
    metadata: '{"project":"McpServer","layer":"services","updated":true}'

All fields in params replace the existing values; supply the full entity body, not a partial patch.

Deleting an Entity

type: request
payload:
  requestId: req-20260409T120011Z-entitydel-001
  method: workflow.graphrag.entities.delete
  params:
    entityId: ent-001

Delete returns an empty result on success. Deleting an entity does not automatically remove its relationships; delete those separately first.

Relationship Management

Relationships are directed edges between two entities with a typed label and optional weight.

Creating a Relationship

type: request
payload:
  requestId: req-20260409T120012Z-relcreate-001
  method: workflow.graphrag.relationships.create
  params:
    sourceEntityId: ent-001
    targetEntityId: ent-002
    relationshipType: validates
    description: TokenService uses JwtValidator to verify token signatures on refresh
    weight: 0.9
    metadata: '{"direction":"bidirectional"}'

Required: sourceEntityId, targetEntityId, relationshipType. Optional: description, weight (default 1.0), metadata.

type: result
payload:
  requestId: req-20260409T120012Z-relcreate-001
  result:
    id: rel-001
    sourceEntityId: ent-001
    targetEntityId: ent-002
    relationshipType: validates
    description: TokenService uses JwtValidator to verify token signatures on refresh
    weight: 0.9
    createdAtUtc: 2026-04-09T12:00:12Z
    updatedAtUtc: 2026-04-09T12:00:12Z

Listing Relationships

type: request
payload:
  requestId: req-20260409T120013Z-rellist-001
  method: workflow.graphrag.relationships.list
  params:
    skip: 0
    take: 50
    entityId: ent-001
    type: validates

Both entityId and type filters are optional. entityId returns all relationships where the entity appears as source or target.

Getting a Single Relationship

type: request
payload:
  requestId: req-20260409T120014Z-relget-001
  method: workflow.graphrag.relationships.get
  params:
    relationshipId: rel-001

Updating a Relationship

type: request
payload:
  requestId: req-20260409T120015Z-relupdate-001
  method: workflow.graphrag.relationships.update
  params:
    relationshipId: rel-001
    sourceEntityId: ent-001
    targetEntityId: ent-002
    relationshipType: validates
    description: Updated description after code review
    weight: 1.0

Supply the full relationship body; all fields replace existing values.

Deleting a Relationship

type: request
payload:
  requestId: req-20260409T120016Z-reldel-001
  method: workflow.graphrag.relationships.delete
  params:
    relationshipId: rel-001

Error Handling

Common error codes for GraphRAG operations:

  • graphrag_disabled — GraphRAG is not enabled for this workspace
  • graphrag_not_indexed — corpus exists but has not been indexed yet; call index first
  • document_not_found — no document with the specified ID
  • entity_not_found — no entity with the specified ID
  • relationship_not_found — no relationship with the specified ID
  • ingestion_error — text could not be chunked or stored
  • index_error — indexing operation failed; check status for lastError

Typical Workflow

To add new knowledge and make it immediately queryable:

  1. Call workflow.graphrag.status to verify GraphRAG is enabled: true and isIndexed: true
  2. Call workflow.graphrag.ingest with the raw text; set triggerReindex: false for batch ingestion
  3. Optionally call workflow.graphrag.entities.create to add curated entities from the text
  4. Optionally call workflow.graphrag.relationships.create to link new entities to existing ones
  5. Call workflow.graphrag.index with force: false once all documents are ingested
  6. Call workflow.graphrag.query with mode: local to verify the new knowledge is retrievable

For large ingestion batches, ingest all documents first, then trigger a single index call at the end to minimize total indexing time.

Install via CLI
npx skills add https://github.com/sharpninja/mcpserver-codex-plugin --skill graphrag-knowledge-graph
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